Job ID = 6507762 SRX = SRX331184 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:02:55 prefetch.2.10.7: 1) Downloading 'SRR947416'... 2020-06-26T13:02:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:03:55 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:03:55 prefetch.2.10.7: 'SRR947416' is valid 2020-06-26T13:03:55 prefetch.2.10.7: 1) 'SRR947416' was downloaded successfully Read 5886071 spots for SRR947416/SRR947416.sra Written 5886071 spots for SRR947416/SRR947416.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: 00:00:55 5886071 reads; of these: 5886071 (100.00%) were unpaired; of these: 585285 (9.94%) aligned 0 times 4440282 (75.44%) aligned exactly 1 time 860504 (14.62%) aligned >1 times 90.06% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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_rmdupse_core] 593437 / 5300786 = 0.1120 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 @ Fri, 26 Jun 2020 22:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.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 @ Fri, 26 Jun 2020 22:06:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:06:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:07:00: 1000000 INFO @ Fri, 26 Jun 2020 22:07:05: 2000000 INFO @ Fri, 26 Jun 2020 22:07:11: 3000000 INFO @ Fri, 26 Jun 2020 22:07:17: 4000000 INFO @ Fri, 26 Jun 2020 22:07:21: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 22:07:21: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 22:07:21: #1 total tags in treatment: 4707349 INFO @ Fri, 26 Jun 2020 22:07:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:07:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:07:21: #1 tags after filtering in treatment: 4707349 INFO @ Fri, 26 Jun 2020 22:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:07:21: #1 finished! INFO @ Fri, 26 Jun 2020 22:07:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:07:21: #2 number of paired peaks: 441 WARNING @ Fri, 26 Jun 2020 22:07:21: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 26 Jun 2020 22:07:21: start model_add_line... INFO @ Fri, 26 Jun 2020 22:07:21: start X-correlation... INFO @ Fri, 26 Jun 2020 22:07:21: end of X-cor INFO @ Fri, 26 Jun 2020 22:07:21: #2 finished! INFO @ Fri, 26 Jun 2020 22:07:21: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 22:07:21: #2 alternative fragment length(s) may be 4,34,93,585 bps INFO @ Fri, 26 Jun 2020 22:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.05_model.r WARNING @ Fri, 26 Jun 2020 22:07:21: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:07:21: #2 You may need to consider one of the other alternative d(s): 4,34,93,585 WARNING @ Fri, 26 Jun 2020 22:07:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:07:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:07:21: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 22:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.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 @ Fri, 26 Jun 2020 22:07:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:07:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:07:29: 1000000 INFO @ Fri, 26 Jun 2020 22:07:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:07:34: 2000000 INFO @ Fri, 26 Jun 2020 22:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.05_summits.bed INFO @ Fri, 26 Jun 2020 22:07:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:07:39: 3000000 INFO @ Fri, 26 Jun 2020 22:07:44: 4000000 INFO @ Fri, 26 Jun 2020 22:07:47: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 22:07:47: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 22:07:47: #1 total tags in treatment: 4707349 INFO @ Fri, 26 Jun 2020 22:07:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:07:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:07:47: #1 tags after filtering in treatment: 4707349 INFO @ Fri, 26 Jun 2020 22:07:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:07:47: #1 finished! INFO @ Fri, 26 Jun 2020 22:07:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:07:48: #2 number of paired peaks: 441 WARNING @ Fri, 26 Jun 2020 22:07:48: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 26 Jun 2020 22:07:48: start model_add_line... INFO @ Fri, 26 Jun 2020 22:07:48: start X-correlation... INFO @ Fri, 26 Jun 2020 22:07:48: end of X-cor INFO @ Fri, 26 Jun 2020 22:07:48: #2 finished! INFO @ Fri, 26 Jun 2020 22:07:48: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 22:07:48: #2 alternative fragment length(s) may be 4,34,93,585 bps INFO @ Fri, 26 Jun 2020 22:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.10_model.r WARNING @ Fri, 26 Jun 2020 22:07:48: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:07:48: #2 You may need to consider one of the other alternative d(s): 4,34,93,585 WARNING @ Fri, 26 Jun 2020 22:07:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:07:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:07:48: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 22:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.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 @ Fri, 26 Jun 2020 22:07:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:07:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:07:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:08:00: 1000000 INFO @ Fri, 26 Jun 2020 22:08:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:08:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:08:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.10_summits.bed INFO @ Fri, 26 Jun 2020 22:08:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:08:06: 2000000 INFO @ Fri, 26 Jun 2020 22:08:12: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:08:17: 4000000 INFO @ Fri, 26 Jun 2020 22:08:21: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 22:08:21: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 22:08:21: #1 total tags in treatment: 4707349 INFO @ Fri, 26 Jun 2020 22:08:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:08:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:08:21: #1 tags after filtering in treatment: 4707349 INFO @ Fri, 26 Jun 2020 22:08:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:08:21: #1 finished! INFO @ Fri, 26 Jun 2020 22:08:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:08:22: #2 number of paired peaks: 441 WARNING @ Fri, 26 Jun 2020 22:08:22: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 26 Jun 2020 22:08:22: start model_add_line... INFO @ Fri, 26 Jun 2020 22:08:22: start X-correlation... INFO @ Fri, 26 Jun 2020 22:08:22: end of X-cor INFO @ Fri, 26 Jun 2020 22:08:22: #2 finished! INFO @ Fri, 26 Jun 2020 22:08:22: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 22:08:22: #2 alternative fragment length(s) may be 4,34,93,585 bps INFO @ Fri, 26 Jun 2020 22:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.20_model.r WARNING @ Fri, 26 Jun 2020 22:08:22: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:08:22: #2 You may need to consider one of the other alternative d(s): 4,34,93,585 WARNING @ Fri, 26 Jun 2020 22:08:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:08:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:08:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331184/SRX331184.20_summits.bed INFO @ Fri, 26 Jun 2020 22:08:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling