Job ID = 14520234 SRX = SRX8398424 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1845105 spots for SRR11848040/SRR11848040.sra Written 1845105 spots for SRR11848040/SRR11848040.sra 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 Multiseed full-index search: 00:01:26 1845105 reads; of these: 1845105 (100.00%) were paired; of these: 326940 (17.72%) aligned concordantly 0 times 1314106 (71.22%) aligned concordantly exactly 1 time 204059 (11.06%) aligned concordantly >1 times ---- 326940 pairs aligned concordantly 0 times; of these: 29686 (9.08%) aligned discordantly 1 time ---- 297254 pairs aligned 0 times concordantly or discordantly; of these: 594508 mates make up the pairs; of these: 572446 (96.29%) aligned 0 times 13838 (2.33%) aligned exactly 1 time 8224 (1.38%) aligned >1 times 84.49% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 98493 / 1518232 = 0.0649 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 18:45:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:45:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:45:37: 1000000 INFO @ Sat, 15 Jan 2022 18:45:45: 2000000 INFO @ Sat, 15 Jan 2022 18:45:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:45:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:45:52: #1 total tags in treatment: 1420233 INFO @ Sat, 15 Jan 2022 18:45:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:45:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:45:52: #1 tags after filtering in treatment: 1134281 INFO @ Sat, 15 Jan 2022 18:45:52: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 15 Jan 2022 18:45:52: #1 finished! INFO @ Sat, 15 Jan 2022 18:45:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:45:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:45:52: #2 number of paired peaks: 109 WARNING @ Sat, 15 Jan 2022 18:45:52: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Jan 2022 18:45:52: start model_add_line... INFO @ Sat, 15 Jan 2022 18:45:52: start X-correlation... INFO @ Sat, 15 Jan 2022 18:45:52: end of X-cor INFO @ Sat, 15 Jan 2022 18:45:52: #2 finished! INFO @ Sat, 15 Jan 2022 18:45:52: #2 predicted fragment length is 9 bps INFO @ Sat, 15 Jan 2022 18:45:52: #2 alternative fragment length(s) may be 4,9,46,55,81,99,128,151,178,258,293,317,350,383,415,494,530,550,584 bps INFO @ Sat, 15 Jan 2022 18:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.05_model.r WARNING @ Sat, 15 Jan 2022 18:45:52: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:45:52: #2 You may need to consider one of the other alternative d(s): 4,9,46,55,81,99,128,151,178,258,293,317,350,383,415,494,530,550,584 WARNING @ Sat, 15 Jan 2022 18:45:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:45:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:45:55: #3 Call peaks for each chromosome... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.05_summits.bed INFO @ Sat, 15 Jan 2022 18:45:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 18:45:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:45:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:46:09: 1000000 INFO @ Sat, 15 Jan 2022 18:46:19: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:46:27: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:46:27: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:46:27: #1 total tags in treatment: 1420233 INFO @ Sat, 15 Jan 2022 18:46:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:46:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:46:27: #1 tags after filtering in treatment: 1134281 INFO @ Sat, 15 Jan 2022 18:46:27: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 15 Jan 2022 18:46:27: #1 finished! INFO @ Sat, 15 Jan 2022 18:46:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:46:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:46:27: #2 number of paired peaks: 109 WARNING @ Sat, 15 Jan 2022 18:46:27: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Jan 2022 18:46:27: start model_add_line... INFO @ Sat, 15 Jan 2022 18:46:27: start X-correlation... INFO @ Sat, 15 Jan 2022 18:46:27: end of X-cor INFO @ Sat, 15 Jan 2022 18:46:27: #2 finished! INFO @ Sat, 15 Jan 2022 18:46:27: #2 predicted fragment length is 9 bps INFO @ Sat, 15 Jan 2022 18:46:27: #2 alternative fragment length(s) may be 4,9,46,55,81,99,128,151,178,258,293,317,350,383,415,494,530,550,584 bps INFO @ Sat, 15 Jan 2022 18:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.10_model.r WARNING @ Sat, 15 Jan 2022 18:46:27: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:46:27: #2 You may need to consider one of the other alternative d(s): 4,9,46,55,81,99,128,151,178,258,293,317,350,383,415,494,530,550,584 WARNING @ Sat, 15 Jan 2022 18:46:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:46:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 18:46:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:46:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:46:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.10_summits.bed INFO @ Sat, 15 Jan 2022 18:46:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:46:37: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:46:44: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:46:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:46:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:46:51: #1 total tags in treatment: 1420233 INFO @ Sat, 15 Jan 2022 18:46:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:46:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:46:51: #1 tags after filtering in treatment: 1134281 INFO @ Sat, 15 Jan 2022 18:46:51: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 15 Jan 2022 18:46:51: #1 finished! INFO @ Sat, 15 Jan 2022 18:46:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:46:51: #2 number of paired peaks: 109 WARNING @ Sat, 15 Jan 2022 18:46:51: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Jan 2022 18:46:51: start model_add_line... INFO @ Sat, 15 Jan 2022 18:46:51: start X-correlation... INFO @ Sat, 15 Jan 2022 18:46:51: end of X-cor INFO @ Sat, 15 Jan 2022 18:46:51: #2 finished! INFO @ Sat, 15 Jan 2022 18:46:51: #2 predicted fragment length is 9 bps INFO @ Sat, 15 Jan 2022 18:46:51: #2 alternative fragment length(s) may be 4,9,46,55,81,99,128,151,178,258,293,317,350,383,415,494,530,550,584 bps INFO @ Sat, 15 Jan 2022 18:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.20_model.r WARNING @ Sat, 15 Jan 2022 18:46:51: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:46:51: #2 You may need to consider one of the other alternative d(s): 4,9,46,55,81,99,128,151,178,258,293,317,350,383,415,494,530,550,584 WARNING @ Sat, 15 Jan 2022 18:46:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:46:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:46:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398424/SRX8398424.20_summits.bed INFO @ Sat, 15 Jan 2022 18:46:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling