anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 anaconda3/5.2.0(77):ERROR:150: Module 'anaconda3/5.2.0' conflicts with the currently loaded module(s) 'anaconda2/5.2.0' anaconda3/5.2.0(77):ERROR:102: Tcl command execution failed: conflict python2 python3 python2-intel python3-intel anaconda2 anaconda3 [2019-06-24 21:23:18] Beginning TopHat run (v2.1.1) ----------------------------------------------- [2019-06-24 21:23:18] Checking for Bowtie Bowtie version: 2.3.4.1 [2019-06-24 21:23:18] Checking for Bowtie index files (genome).. [2019-06-24 21:23:18] Checking for reference FASTA file [2019-06-24 21:23:18] Generating SAM header for Bowtie2Index/genome [2019-06-24 21:23:21] Reading known junctions from GTF file [2019-06-24 21:23:24] Preparing reads left reads: min. length=32, max. length=36, 13355729 kept reads (77135 discarded) right reads: min. length=32, max. length=36, 12996020 kept reads (436844 discarded) [2019-06-24 21:28:35] Building transcriptome data files /scratch/7056804.1.linga/tophat2/tmp/RefSeq_GeneBody [2019-06-24 21:28:50] Building Bowtie index from RefSeq_GeneBody.fa [2019-06-24 21:34:45] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 [2019-06-24 21:38:46] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 Traceback (most recent call last): File "/share/pkg.7/tophat/2.1.1/install/bin/tophat", line 4107, in sys.exit(main()) File "/share/pkg.7/tophat/2.1.1/install/bin/tophat", line 4073, in main user_supplied_deletions) File "/share/pkg.7/tophat/2.1.1/install/bin/tophat", line 3458, in spliced_alignment map2gtf(params, sam_header_filename, ref_fasta, left_reads, right_reads) File "/share/pkg.7/tophat/2.1.1/install/bin/tophat", line 3344, in map2gtf "", _reads_vs_T) File "/share/pkg.7/tophat/2.1.1/install/bin/tophat", line 2443, in bowtie print >> run_log, shellcmd IOError: [Errno 28] No space left on device open: No such file or directory [main_samview] fail to open "/scratch/7056804.1.linga/tophat2/accepted_hits.bam" for reading. open: No such file or directory [main_samview] fail to open "/scratch/7056804.1.linga/tophat2/accepted_hits.bam" for reading. open: No such file or directory [bam_index_build2] fail to open the BAM file. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). open: No such file or directory samtools: bam_stat.c:59: bam_flagstat: Assertion `fp' failed. /var/spool/sge/scc-kb5/job_scripts/7056804: line 418: 22241 Aborted samtools flagstat ${OUTPUT_DIR}/accepted_hits.bam > ${OUTPUT_DIR}/statistics_for_all_accepted_reads.txt open: No such file or directory samtools: bam_stat.c:59: bam_flagstat: Assertion `fp' failed. /var/spool/sge/scc-kb5/job_scripts/7056804: line 419: 22242 Aborted samtools flagstat ${OUTPUT_DIR}/unmapped.bam > ${OUTPUT_DIR}/statistics_for_unmapped_reads.txt open: No such file or directory [main_samview] fail to open "/scratch/7056804.1.linga/tophat2/accepted_hits.bam" for reading. wc: write error [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "primary.bam". [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [main_samview] fail to read the header from "primary.bam". [samopen] no @SQ lines in the header. [sam_read1] missing header? Abort! [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). /var/spool/sge/scc-kb5/job_scripts/7056804: line 446: 22254 Segmentation fault samtools sort temp4.bam 'primary_unique' open: No such file or directory [bam_index_build2] fail to open the BAM file. open: No such file or directory samtools: bam_stat.c:59: bam_flagstat: Assertion `fp' failed. /var/spool/sge/scc-kb5/job_scripts/7056804: line 452: 22262 Aborted samtools flagstat 'primary_unique'.bam > statistics_for_'primary_unique'_reads.txt rm: cannot remove '/scratch/7056804.1.linga/tophat2/accepted_hits.bam': No such file or directory rm: cannot remove '/scratch/7056804.1.linga/tophat2/accepted_hits.bam.bai': No such file or directory rm: cannot remove '/scratch/7056804.1.linga/tophat2/primary.bam.bai': No such file or directory rm: cannot remove '/scratch/7056804.1.linga/tophat2/unmapped.bam': No such file or directory open: No such file or directory [main_samview] fail to open "IC57-6_primary_unique.bam" for reading. open: No such file or directory [main_samview] fail to open "IC57-6_primary_unique.bam" for reading. /var/spool/sge/scc-kb5/job_scripts/7056804: line 528: echo: write error: No space left on device /var/spool/sge/scc-kb5/job_scripts/7056804: line 530: echo: write error: No space left on device