Job ID = 16435251 SRX = SRX9091664 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Warning: skipping mate #1 of read 'SRR12608195.1593400 1593400 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608195.1593400 1593400 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608195.1593400 1593400 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608195.1593400 1593400 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608195.21548071 21548071 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608195.21548071 21548071 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608195.40338489 40338489 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608195.40338489 40338489 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608195.44851871 44851871 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608195.44851871 44851871 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608195.52515313 52515313 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608195.52515313 52515313 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608195.52515313 52515313 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608195.52515313 52515313 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 44 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 50934913 / 51710035 = 0.9850 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:53:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 11:53:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:53:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:53:31: 1000000 INFO @ Tue, 02 Aug 2022 11:53:36: 2000000 INFO @ Tue, 02 Aug 2022 11:53:38: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:53:38: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:53:38: #1 total tags in treatment: 771685 INFO @ Tue, 02 Aug 2022 11:53:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:53:38: #1 tags after filtering in treatment: 510412 INFO @ Tue, 02 Aug 2022 11:53:38: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 11:53:38: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:38: #2 number of paired peaks: 1174 INFO @ Tue, 02 Aug 2022 11:53:38: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:38: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:38: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:38: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:38: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 11:53:38: #2 alternative fragment length(s) may be 108,590 bps INFO @ Tue, 02 Aug 2022 11:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.05_model.r WARNING @ Tue, 02 Aug 2022 11:53:38: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:53:38: #2 You may need to consider one of the other alternative d(s): 108,590 WARNING @ Tue, 02 Aug 2022 11:53:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:53:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.05_summits.bed INFO @ Tue, 02 Aug 2022 11:53:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (638 records, 4 fields): 68 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 11:53:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:53:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:54:00: 1000000 INFO @ Tue, 02 Aug 2022 11:54:06: 2000000 INFO @ Tue, 02 Aug 2022 11:54:07: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:54:07: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:54:07: #1 total tags in treatment: 771685 INFO @ Tue, 02 Aug 2022 11:54:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:54:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:54:08: #1 tags after filtering in treatment: 510412 INFO @ Tue, 02 Aug 2022 11:54:08: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 11:54:08: #1 finished! INFO @ Tue, 02 Aug 2022 11:54:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:54:08: #2 number of paired peaks: 1174 INFO @ Tue, 02 Aug 2022 11:54:08: start model_add_line... INFO @ Tue, 02 Aug 2022 11:54:08: start X-correlation... INFO @ Tue, 02 Aug 2022 11:54:08: end of X-cor INFO @ Tue, 02 Aug 2022 11:54:08: #2 finished! INFO @ Tue, 02 Aug 2022 11:54:08: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 11:54:08: #2 alternative fragment length(s) may be 108,590 bps INFO @ Tue, 02 Aug 2022 11:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.10_model.r WARNING @ Tue, 02 Aug 2022 11:54:08: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:54:08: #2 You may need to consider one of the other alternative d(s): 108,590 WARNING @ Tue, 02 Aug 2022 11:54:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:54:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:54:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.10_summits.bed INFO @ Tue, 02 Aug 2022 11:54:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (413 records, 4 fields): 67 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 11:54:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:54:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:54:30: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:54:35: 2000000 INFO @ Tue, 02 Aug 2022 11:54:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:54:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:54:37: #1 total tags in treatment: 771685 INFO @ Tue, 02 Aug 2022 11:54:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:54:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:54:37: #1 tags after filtering in treatment: 510412 INFO @ Tue, 02 Aug 2022 11:54:37: #1 Redundant rate of treatment: 0.34 INFO @ Tue, 02 Aug 2022 11:54:37: #1 finished! INFO @ Tue, 02 Aug 2022 11:54:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:54:37: #2 number of paired peaks: 1174 INFO @ Tue, 02 Aug 2022 11:54:37: start model_add_line... INFO @ Tue, 02 Aug 2022 11:54:37: start X-correlation... INFO @ Tue, 02 Aug 2022 11:54:37: end of X-cor INFO @ Tue, 02 Aug 2022 11:54:37: #2 finished! INFO @ Tue, 02 Aug 2022 11:54:37: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 11:54:37: #2 alternative fragment length(s) may be 108,590 bps INFO @ Tue, 02 Aug 2022 11:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.20_model.r WARNING @ Tue, 02 Aug 2022 11:54:37: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:54:37: #2 You may need to consider one of the other alternative d(s): 108,590 WARNING @ Tue, 02 Aug 2022 11:54:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:54:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:54:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:54:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091664/SRX9091664.20_summits.bed INFO @ Tue, 02 Aug 2022 11:54:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 37 millis CompletedMACS2peakCalling