[stdout]
chunk_reads vVERSION
chunks: [("R1", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz", false), ("R2", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz", false), ("I1", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz", false)]
opening: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz"
opening: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz"
got recs: 50000000
opening: "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz"
got recs: 50000000
got recs: 50000000
[("R1", ["/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0000.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0001.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0002.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0003.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0004.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0005.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0006.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0007.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0008.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0009.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R1-0010.fastq.lz4"]), ("R2", ["/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0000.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0001.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0002.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0003.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0004.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0005.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0006.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0007.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0008.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0009.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/R2-0010.fastq.lz4"]), ("I1", ["/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0000.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0001.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0002.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0003.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0004.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0005.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0006.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0007.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0008.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0009.fastq.lz4", "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/I1-0010.fastq.lz4"])]
running chunk reads: [['chunk_reads', '--reads-per-fastq', '5000000', '/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/Chow_1_Test/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk1-u8c0aa70665/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']]
{u'gem_group': 1, u'library_type': u'Gene Expression', u'read_group': u'Chow_1_Test:0:1:HMVM3BBXX:8', u'subsample_rate': 1.0, u'library_id': u'0', u'reads_interleaved': False, u'chemistry': {u'si_read_offset': 0, u'strandedness': u'+', u'umi_read_offset': 16, u'barcode_read_type': u'R1', u'umi_read_type': u'R1', u'barcode_read_length': 16, u'rna_read_type': u'R2', u'barcode_whitelist': u'737K-august-2016', u'si_read_type': u'I1', u'rna_read_length': None, u'description': u"Single Cell 3' v2", u'rna_read_offset': 0, u'barcode_read_offset': 0, u'rna_read2_type': None, u'endedness': u'three_prime', u'name': u'SC3Pv2', u'umi_read_length': 10, u'si_read_length': None, u'read_type_to_bcl2fastq_filename': {u'I1': u'I1', u'I2': None, u'R1': u'R1', u'R2': u'R2'}, u'rna_read2_length': None, u'rna_read2_offset': 0, u'read_type_to_bcl_processor_filename': {u'I1': u'I1', u'I2': None, u'R1': u'RA', u'R2': None}}, u'read_chunks': {u'I1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz', u'I2': None, u'R1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz', u'R2': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz'}}
{u'gem_group': 1, u'library_type': u'Gene Expression', u'read_group': u'Chow_1_Test:0:1:HMVM3BBXX:8', u'subsample_rate': 1.0, u'library_id': u'0', u'read_chunks': {u'I1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz', u'I2': None, u'R1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz', u'R2': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz'}, u'chemistry': {u'si_read_offset': 0, u'strandedness': u'+', u'umi_read_offset': 16, u'barcode_read_type': u'R1', u'umi_read_type': u'R1', u'barcode_read_length': 16, u'rna_read_type': u'R2', u'barcode_whitelist': u'737K-august-2016', u'si_read_type': u'I1', u'rna_read_length': None, u'description': u"Single Cell 3' v2", u'rna_read_offset': 0, u'barcode_read_offset': 0, u'rna_read2_type': None, u'endedness': u'three_prime', u'name': u'SC3Pv2', u'umi_read_length': 10, u'si_read_length': None, u'read_type_to_bcl2fastq_filename': {u'I1': u'I1', u'I2': None, u'R1': u'R1', u'R2': u'R2'}, u'rna_read2_length': None, u'rna_read2_offset': 0, u'read_type_to_bcl_processor_filename': {u'I1': u'I1', u'I2': None, u'R1': u'RA', u'R2': None}}, u'reads_interleaved': False}
{u'gem_group': 1, u'library_type': u'Gene Expression', u'read_group': u'Chow_1_Test:0:1:HMVM3BBXX:8', u'subsample_rate': 1.0, u'library_id': u'0', u'reads_interleaved': False, u'chemistry': {u'si_read_offset': 0, u'strandedness': u'+', u'umi_read_offset': 16, u'barcode_read_type': u'R1', u'umi_read_type': u'R1', u'barcode_read_length': 16, u'rna_read_type': u'R2', u'barcode_whitelist': u'737K-august-2016', u'si_read_type': u'I1', u'rna_read_length': None, u'description': u"Single Cell 3' v2", u'rna_read_offset': 0, u'barcode_read_offset': 0, u'rna_read2_type': None, u'endedness': u'three_prime', u'name': u'SC3Pv2', u'umi_read_length': 10, u'si_read_length': None, u'read_type_to_bcl2fastq_filename': {u'I1': u'I1', u'I2': None, u'R1': u'R1', u'R2': u'R2'}, u'rna_read2_length': None, u'rna_read2_offset': 0, u'read_type_to_bcl_processor_filename': {u'I1': u'I1', u'I2': None, u'R1': u'RA', u'R2': None}}, u'read_chunks': {u'I1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz', u'I2': None, u'R1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz', u'R2': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz'}}
{u'gem_group': 1, u'library_type': u'Gene Expression', u'read_group': u'Chow_1_Test:0:1:HMVM3BBXX:8', u'subsample_rate': 1.0, u'library_id': u'0', u'read_chunks': {u'I1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz', u'I2': None, u'R1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz', u'R2': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz'}, u'chemistry': {u'si_read_offset': 0, u'strandedness': u'+', u'umi_read_offset': 16, u'barcode_read_type': u'R1', u'umi_read_type': u'R1', u'barcode_read_length': 16, u'rna_read_type': u'R2', u'barcode_whitelist': u'737K-august-2016', u'si_read_type': u'I1', u'rna_read_length': None, u'description': u"Single Cell 3' v2", u'rna_read_offset': 0, u'barcode_read_offset': 0, u'rna_read2_type': None, u'endedness': u'three_prime', u'name': u'SC3Pv2', u'umi_read_length': 10, u'si_read_length': None, u'read_type_to_bcl2fastq_filename': {u'I1': u'I1', u'I2': None, u'R1': u'R1', u'R2': u'R2'}, u'rna_read2_length': None, u'rna_read2_offset': 0, u'read_type_to_bcl_processor_filename': {u'I1': u'I1', u'I2': None, u'R1': u'RA', u'R2': None}}, u'reads_interleaved': False}
{u'gem_group': 1, u'library_type': u'Gene Expression', u'read_group': u'Chow_1_Test:0:1:HMVM3BBXX:8', u'subsample_rate': 1.0, u'library_id': u'0', u'reads_interleaved': False, u'chemistry': {u'si_read_offset': 0, u'strandedness': u'+', u'umi_read_offset': 16, u'barcode_read_type': u'R1', u'umi_read_type': u'R1', u'barcode_read_length': 16, u'rna_read_type': u'R2', u'barcode_whitelist': u'737K-august-2016', u'si_read_type': u'I1', u'rna_read_length': None, u'description': u"Single Cell 3' v2", u'rna_read_offset': 0, u'barcode_read_offset': 0, u'rna_read2_type': None, u'endedness': u'three_prime', u'name': u'SC3Pv2', u'umi_read_length': 10, u'si_read_length': None, u'read_type_to_bcl2fastq_filename': {u'I1': u'I1', u'I2': None, u'R1': u'R1', u'R2': u'R2'}, u'rna_read2_length': None, u'rna_read2_offset': 0, u'read_type_to_bcl_processor_filename': {u'I1': u'I1', u'I2': None, u'R1': u'RA', u'R2': None}}, u'read_chunks': {u'I1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_I1_002.fastq.gz', u'I2': None, u'R1': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R1_002.fastq.gz', u'R2': u'/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/NASH/data/Chow1/10X_Chow_1/CHOW_95239_MissingLibrary_1_HMVM3BBXX/bamtofastq_S1_L008_R2_002.fastq.gz'}}
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