Job ID = 6368663 SRX = SRX529223 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:42 prefetch.2.10.7: 1) Downloading 'SRR1265827'... 2020-06-16T00:30:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:21 prefetch.2.10.7: 1) 'SRR1265827' was downloaded successfully 2020-06-16T00:39:21 prefetch.2.10.7: 'SRR1265827' has 0 unresolved dependencies Read 40075123 spots for SRR1265827/SRR1265827.sra Written 40075123 spots for SRR1265827/SRR1265827.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: 00:14:09 40075123 reads; of these: 40075123 (100.00%) were unpaired; of these: 1275997 (3.18%) aligned 0 times 32481734 (81.05%) aligned exactly 1 time 6317392 (15.76%) aligned >1 times 96.82% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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 16 files... [bam_rmdupse_core] 20131447 / 38799126 = 0.5189 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 10:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.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 10:08:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:08:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:08:55: 1000000 INFO @ Tue, 16 Jun 2020 10:09:03: 2000000 INFO @ Tue, 16 Jun 2020 10:09:10: 3000000 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 10:09:18: 4000000 INFO @ Tue, 16 Jun 2020 10:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.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 10:09:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:27: 5000000 INFO @ Tue, 16 Jun 2020 10:09:28: 1000000 INFO @ Tue, 16 Jun 2020 10:09:36: 6000000 INFO @ Tue, 16 Jun 2020 10:09:38: 2000000 INFO @ Tue, 16 Jun 2020 10:09:46: 7000000 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 10:09:48: 3000000 INFO @ Tue, 16 Jun 2020 10:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.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 10:09:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:55: 8000000 INFO @ Tue, 16 Jun 2020 10:09:58: 1000000 INFO @ Tue, 16 Jun 2020 10:09:58: 4000000 INFO @ Tue, 16 Jun 2020 10:10:05: 9000000 INFO @ Tue, 16 Jun 2020 10:10:07: 2000000 INFO @ Tue, 16 Jun 2020 10:10:08: 5000000 INFO @ Tue, 16 Jun 2020 10:10:14: 10000000 INFO @ Tue, 16 Jun 2020 10:10:17: 3000000 INFO @ Tue, 16 Jun 2020 10:10:19: 6000000 INFO @ Tue, 16 Jun 2020 10:10:24: 11000000 INFO @ Tue, 16 Jun 2020 10:10:26: 4000000 INFO @ Tue, 16 Jun 2020 10:10:29: 7000000 INFO @ Tue, 16 Jun 2020 10:10:34: 12000000 INFO @ Tue, 16 Jun 2020 10:10:36: 5000000 INFO @ Tue, 16 Jun 2020 10:10:39: 8000000 INFO @ Tue, 16 Jun 2020 10:10:43: 13000000 INFO @ Tue, 16 Jun 2020 10:10:46: 6000000 INFO @ Tue, 16 Jun 2020 10:10:50: 9000000 INFO @ Tue, 16 Jun 2020 10:10:53: 14000000 INFO @ Tue, 16 Jun 2020 10:10:56: 7000000 INFO @ Tue, 16 Jun 2020 10:11:00: 10000000 INFO @ Tue, 16 Jun 2020 10:11:03: 15000000 INFO @ Tue, 16 Jun 2020 10:11:06: 8000000 INFO @ Tue, 16 Jun 2020 10:11:10: 11000000 INFO @ Tue, 16 Jun 2020 10:11:13: 16000000 INFO @ Tue, 16 Jun 2020 10:11:15: 9000000 INFO @ Tue, 16 Jun 2020 10:11:21: 12000000 INFO @ Tue, 16 Jun 2020 10:11:22: 17000000 INFO @ Tue, 16 Jun 2020 10:11:25: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:11:31: 13000000 INFO @ Tue, 16 Jun 2020 10:11:32: 18000000 INFO @ Tue, 16 Jun 2020 10:11:35: 11000000 INFO @ Tue, 16 Jun 2020 10:11:38: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:11:38: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:11:38: #1 total tags in treatment: 18667679 INFO @ Tue, 16 Jun 2020 10:11:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:11:38: #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 10:11:39: #1 tags after filtering in treatment: 18667679 INFO @ Tue, 16 Jun 2020 10:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:11:39: #1 finished! INFO @ Tue, 16 Jun 2020 10:11:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:11:40: #2 number of paired peaks: 308 WARNING @ Tue, 16 Jun 2020 10:11:40: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 16 Jun 2020 10:11:40: start model_add_line... INFO @ Tue, 16 Jun 2020 10:11:40: start X-correlation... INFO @ Tue, 16 Jun 2020 10:11:40: end of X-cor INFO @ Tue, 16 Jun 2020 10:11:40: #2 finished! INFO @ Tue, 16 Jun 2020 10:11:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:11:40: #2 alternative fragment length(s) may be 1,29,47,548,578 bps INFO @ Tue, 16 Jun 2020 10:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.05_model.r WARNING @ Tue, 16 Jun 2020 10:11:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:11:40: #2 You may need to consider one of the other alternative d(s): 1,29,47,548,578 WARNING @ Tue, 16 Jun 2020 10:11:40: #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 10:11:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:11:41: 14000000 INFO @ Tue, 16 Jun 2020 10:11:46: 12000000 INFO @ Tue, 16 Jun 2020 10:11:52: 15000000 INFO @ Tue, 16 Jun 2020 10:11:55: 13000000 INFO @ Tue, 16 Jun 2020 10:12:02: 16000000 INFO @ Tue, 16 Jun 2020 10:12:05: 14000000 INFO @ Tue, 16 Jun 2020 10:12:12: 17000000 INFO @ Tue, 16 Jun 2020 10:12:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:12:15: 15000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:12:22: 18000000 INFO @ Tue, 16 Jun 2020 10:12:25: 16000000 INFO @ Tue, 16 Jun 2020 10:12:29: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:12:29: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:12:29: #1 total tags in treatment: 18667679 INFO @ Tue, 16 Jun 2020 10:12:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:29: #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 10:12:29: #1 tags after filtering in treatment: 18667679 INFO @ Tue, 16 Jun 2020 10:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:12:29: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:12:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.05_summits.bed INFO @ Tue, 16 Jun 2020 10:12:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:12:30: #2 number of paired peaks: 308 WARNING @ Tue, 16 Jun 2020 10:12:30: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:30: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:31: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:31: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:31: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:12:31: #2 alternative fragment length(s) may be 1,29,47,548,578 bps INFO @ Tue, 16 Jun 2020 10:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.10_model.r WARNING @ Tue, 16 Jun 2020 10:12:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:12:31: #2 You may need to consider one of the other alternative d(s): 1,29,47,548,578 WARNING @ Tue, 16 Jun 2020 10:12:31: #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 10:12:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:12:34: 17000000 INFO @ Tue, 16 Jun 2020 10:12:42: 18000000 INFO @ Tue, 16 Jun 2020 10:12:47: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 10:12:47: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 10:12:47: #1 total tags in treatment: 18667679 INFO @ Tue, 16 Jun 2020 10:12:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:47: #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 10:12:47: #1 tags after filtering in treatment: 18667679 INFO @ Tue, 16 Jun 2020 10:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:12:47: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:49: #2 number of paired peaks: 308 WARNING @ Tue, 16 Jun 2020 10:12:49: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:49: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:49: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:49: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:49: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:49: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:12:49: #2 alternative fragment length(s) may be 1,29,47,548,578 bps INFO @ Tue, 16 Jun 2020 10:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.20_model.r WARNING @ Tue, 16 Jun 2020 10:12:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:12:49: #2 You may need to consider one of the other alternative d(s): 1,29,47,548,578 WARNING @ Tue, 16 Jun 2020 10:12:49: #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 10:12:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:13:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.10_summits.bed INFO @ Tue, 16 Jun 2020 10:13:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:13:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529223/SRX529223.20_summits.bed INFO @ Tue, 16 Jun 2020 10:13:37: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling