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 cp: error writing './Bowtie2Index/genome.fa': No space left on device cp: failed to extend './Bowtie2Index/genome.fa': No space left on device cp: error writing './RefSeq_GeneBody.gtf': No space left on device cp: failed to extend './RefSeq_GeneBody.gtf': No space left on device mkdir: cannot create directory '/scratch/7056752.1.linga/tophat2': No space left on device 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 3885, in main prepare_output_dir() File "/share/pkg.7/tophat/2.1.1/install/bin/tophat", line 1244, in prepare_output_dir os.mkdir(output_dir) OSError: [Errno 28] No space left on device: '/scratch/7056752.1.linga/tophat2/' /var/spool/sge/scc-kb5/job_scripts/7056752: line 408: /scratch/7056752.1.linga/tophat2/non_primary.bam: No such file or directory /var/spool/sge/scc-kb5/job_scripts/7056752: line 411: /scratch/7056752.1.linga/tophat2/primary.bam: No such file or directory open: No such file or directory [bam_index_build2] fail to open the BAM file. open: No such file or directory [bam_index_build2] fail to open the BAM file. /var/spool/sge/scc-kb5/job_scripts/7056752: line 416: /scratch/7056752.1.linga/tophat2/statistics_for_nonprimary_reads.txt: No such file or directory /var/spool/sge/scc-kb5/job_scripts/7056752: line 417: /scratch/7056752.1.linga/tophat2/statistics_for_primary_reads.txt: No such file or directory /var/spool/sge/scc-kb5/job_scripts/7056752: line 418: /scratch/7056752.1.linga/tophat2/statistics_for_all_accepted_reads.txt: No such file or directory /var/spool/sge/scc-kb5/job_scripts/7056752: line 419: /scratch/7056752.1.linga/tophat2/statistics_for_unmapped_reads.txt: No such file or directory open: No such file or directory [main_samview] fail to open "/scratch/7056752.1.linga/tophat2/accepted_hits.bam" for reading. wc: write error /var/spool/sge/scc-kb5/job_scripts/7056752: line 424: cd: /scratch/7056752.1.linga/tophat2: No such file or directory open: No such file or directory [main_samview] fail to open "primary.bam" for reading. open: No such file or directory [main_samview] fail to open "primary.bam" for reading. [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/7056752: line 446: 64465 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/7056752: line 452: 64467 Aborted samtools flagstat 'primary_unique'.bam > statistics_for_'primary_unique'_reads.txt rm: cannot remove '/scratch/7056752.1.linga/tophat2/non_primary.bam': No such file or directory rm: cannot remove '/scratch/7056752.1.linga/tophat2/accepted_hits.bam': No such file or directory rm: cannot remove '/scratch/7056752.1.linga/tophat2/accepted_hits.bam.bai': No such file or directory rm: cannot remove '/scratch/7056752.1.linga/tophat2/primary.bam': No such file or directory rm: cannot remove '/scratch/7056752.1.linga/tophat2/primary.bam.bai': No such file or directory rm: cannot remove '/scratch/7056752.1.linga/tophat2/unmapped.bam': No such file or directory mv: cannot stat '/scratch/7056752.1.linga/tophat2/*': No such file or directory /var/spool/sge/scc-kb5/job_scripts/7056752: line 504: cd: /scratch/7056752.1.linga/tophat2: No such file or directory touch: cannot touch '/scratch/7056752.1.linga/tophat2/N-3_spliced_read_counts.txt': No such file or directory open: No such file or directory [main_samview] fail to open "N-3_primary_unique.bam" for reading. open: No such file or directory [main_samview] fail to open "N-3_primary_unique.bam" for reading. /var/spool/sge/scc-kb5/job_scripts/7056752: line 528: /scratch/7056752.1.linga/tophat2/N-3_spliced_read_counts.txt: No such file or directory /var/spool/sge/scc-kb5/job_scripts/7056752: line 530: /scratch/7056752.1.linga/tophat2/N-3_spliced_read_counts.txt: No such file or directory cp: cannot stat '*.txt': No such file or directory cp: cannot stat '/scratch/7056752.1.linga/tophat2': No such file or directory