Job ID = 6366874 SRX = SRX245917 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:46 prefetch.2.10.7: 1) Downloading 'SRR765974'... 2020-06-15T23:14:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:31 prefetch.2.10.7: 1) 'SRR765974' was downloaded successfully Read 26558615 spots for SRR765974/SRR765974.sra Written 26558615 spots for SRR765974/SRR765974.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: 00:04:30 26558615 reads; of these: 26558615 (100.00%) were unpaired; of these: 2296372 (8.65%) aligned 0 times 19973004 (75.20%) aligned exactly 1 time 4289239 (16.15%) aligned >1 times 91.35% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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 8 files... [bam_rmdupse_core] 3744075 / 24262243 = 0.1543 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:28:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.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, 16 Jun 2020 08:28:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:48: 1000000 INFO @ Tue, 16 Jun 2020 08:28:52: 2000000 INFO @ Tue, 16 Jun 2020 08:28:57: 3000000 INFO @ Tue, 16 Jun 2020 08:29:01: 4000000 INFO @ Tue, 16 Jun 2020 08:29:06: 5000000 INFO @ Tue, 16 Jun 2020 08:29:10: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:29:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.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, 16 Jun 2020 08:29:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:14: 7000000 INFO @ Tue, 16 Jun 2020 08:29:18: 1000000 INFO @ Tue, 16 Jun 2020 08:29:19: 8000000 INFO @ Tue, 16 Jun 2020 08:29:22: 2000000 INFO @ Tue, 16 Jun 2020 08:29:23: 9000000 INFO @ Tue, 16 Jun 2020 08:29:27: 3000000 INFO @ Tue, 16 Jun 2020 08:29:28: 10000000 INFO @ Tue, 16 Jun 2020 08:29:31: 4000000 INFO @ Tue, 16 Jun 2020 08:29:32: 11000000 INFO @ Tue, 16 Jun 2020 08:29:36: 5000000 INFO @ Tue, 16 Jun 2020 08:29:37: 12000000 INFO @ Tue, 16 Jun 2020 08:29:40: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:29:42: 13000000 INFO @ Tue, 16 Jun 2020 08:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.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, 16 Jun 2020 08:29:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:45: 7000000 INFO @ Tue, 16 Jun 2020 08:29:47: 14000000 INFO @ Tue, 16 Jun 2020 08:29:48: 1000000 INFO @ Tue, 16 Jun 2020 08:29:49: 8000000 INFO @ Tue, 16 Jun 2020 08:29:51: 15000000 INFO @ Tue, 16 Jun 2020 08:29:53: 2000000 INFO @ Tue, 16 Jun 2020 08:29:54: 9000000 INFO @ Tue, 16 Jun 2020 08:29:56: 16000000 INFO @ Tue, 16 Jun 2020 08:29:58: 3000000 INFO @ Tue, 16 Jun 2020 08:29:58: 10000000 INFO @ Tue, 16 Jun 2020 08:30:01: 17000000 INFO @ Tue, 16 Jun 2020 08:30:03: 11000000 INFO @ Tue, 16 Jun 2020 08:30:03: 4000000 INFO @ Tue, 16 Jun 2020 08:30:06: 18000000 INFO @ Tue, 16 Jun 2020 08:30:07: 12000000 INFO @ Tue, 16 Jun 2020 08:30:08: 5000000 INFO @ Tue, 16 Jun 2020 08:30:11: 19000000 INFO @ Tue, 16 Jun 2020 08:30:13: 6000000 INFO @ Tue, 16 Jun 2020 08:30:13: 13000000 INFO @ Tue, 16 Jun 2020 08:30:16: 20000000 INFO @ Tue, 16 Jun 2020 08:30:17: 14000000 INFO @ Tue, 16 Jun 2020 08:30:18: 7000000 INFO @ Tue, 16 Jun 2020 08:30:19: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:30:19: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:30:19: #1 total tags in treatment: 20518168 INFO @ Tue, 16 Jun 2020 08:30:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:30:19: #1 tags after filtering in treatment: 20518168 INFO @ Tue, 16 Jun 2020 08:30:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:20: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 08:30:20: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:21: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:30:21: #2 alternative fragment length(s) may be 2,31,88,488 bps INFO @ Tue, 16 Jun 2020 08:30:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:21: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:21: #2 You may need to consider one of the other alternative d(s): 2,31,88,488 WARNING @ Tue, 16 Jun 2020 08:30:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:30:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:22: 15000000 INFO @ Tue, 16 Jun 2020 08:30:22: 8000000 INFO @ Tue, 16 Jun 2020 08:30:26: 16000000 INFO @ Tue, 16 Jun 2020 08:30:26: 9000000 INFO @ Tue, 16 Jun 2020 08:30:31: 17000000 INFO @ Tue, 16 Jun 2020 08:30:31: 10000000 INFO @ Tue, 16 Jun 2020 08:30:35: 18000000 INFO @ Tue, 16 Jun 2020 08:30:35: 11000000 INFO @ Tue, 16 Jun 2020 08:30:40: 12000000 INFO @ Tue, 16 Jun 2020 08:30:40: 19000000 INFO @ Tue, 16 Jun 2020 08:30:44: 20000000 INFO @ Tue, 16 Jun 2020 08:30:45: 13000000 INFO @ Tue, 16 Jun 2020 08:30:47: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:30:47: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:30:47: #1 total tags in treatment: 20518168 INFO @ Tue, 16 Jun 2020 08:30:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:30:47: #1 tags after filtering in treatment: 20518168 INFO @ Tue, 16 Jun 2020 08:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:48: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 08:30:48: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:49: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:30:49: #2 alternative fragment length(s) may be 2,31,88,488 bps INFO @ Tue, 16 Jun 2020 08:30:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:49: #2 You may need to consider one of the other alternative d(s): 2,31,88,488 WARNING @ Tue, 16 Jun 2020 08:30:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:30:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:50: 14000000 INFO @ Tue, 16 Jun 2020 08:30:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:55: 15000000 INFO @ Tue, 16 Jun 2020 08:31:00: 16000000 INFO @ Tue, 16 Jun 2020 08:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:05: 17000000 INFO @ Tue, 16 Jun 2020 08:31:10: 18000000 INFO @ Tue, 16 Jun 2020 08:31:15: 19000000 INFO @ Tue, 16 Jun 2020 08:31:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:21: 20000000 INFO @ Tue, 16 Jun 2020 08:31:24: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:31:24: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:31:24: #1 total tags in treatment: 20518168 INFO @ Tue, 16 Jun 2020 08:31:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:31:25: #1 tags after filtering in treatment: 20518168 INFO @ Tue, 16 Jun 2020 08:31:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:26: #2 number of paired peaks: 131 WARNING @ Tue, 16 Jun 2020 08:31:26: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:26: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:31:26: #2 alternative fragment length(s) may be 2,31,88,488 bps INFO @ Tue, 16 Jun 2020 08:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:26: #2 You may need to consider one of the other alternative d(s): 2,31,88,488 WARNING @ Tue, 16 Jun 2020 08:31:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:31:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245917/SRX245917.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:11: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。