Job ID = 6368365 SRX = SRX495045 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:07:24 prefetch.2.10.7: 1) Downloading 'SRR1198577'... 2020-06-16T00:07:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:09:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:09:52 prefetch.2.10.7: 1) 'SRR1198577' was downloaded successfully Read 13809537 spots for SRR1198577/SRR1198577.sra Written 13809537 spots for SRR1198577/SRR1198577.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: 00:02:16 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268854 (16.43%) aligned 0 times 9710133 (70.31%) aligned exactly 1 time 1830550 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 1987862 / 11540683 = 0.1722 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 09:15:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.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 09:15:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:49: 1000000 INFO @ Tue, 16 Jun 2020 09:15:54: 2000000 INFO @ Tue, 16 Jun 2020 09:16:00: 3000000 INFO @ Tue, 16 Jun 2020 09:16:05: 4000000 INFO @ Tue, 16 Jun 2020 09:16:10: 5000000 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 09:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.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 09:16:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:15: 6000000 INFO @ Tue, 16 Jun 2020 09:16:20: 1000000 INFO @ Tue, 16 Jun 2020 09:16:20: 7000000 INFO @ Tue, 16 Jun 2020 09:16:26: 8000000 INFO @ Tue, 16 Jun 2020 09:16:26: 2000000 INFO @ Tue, 16 Jun 2020 09:16:31: 9000000 INFO @ Tue, 16 Jun 2020 09:16:32: 3000000 INFO @ Tue, 16 Jun 2020 09:16:34: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:16:34: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:16:34: #1 total tags in treatment: 9552821 INFO @ Tue, 16 Jun 2020 09:16:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:34: #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 09:16:34: #1 tags after filtering in treatment: 9552821 INFO @ Tue, 16 Jun 2020 09:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:35: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 09:16:35: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:35: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:16:35: #2 alternative fragment length(s) may be 2,38,571,595 bps INFO @ Tue, 16 Jun 2020 09:16:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:35: #2 You may need to consider one of the other alternative d(s): 2,38,571,595 WARNING @ Tue, 16 Jun 2020 09:16:35: #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 09:16:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:38: 4000000 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 09:16:44: 5000000 INFO @ Tue, 16 Jun 2020 09:16:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.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 09:16:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:49: 1000000 INFO @ Tue, 16 Jun 2020 09:16:50: 6000000 INFO @ Tue, 16 Jun 2020 09:16:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:55: 2000000 INFO @ Tue, 16 Jun 2020 09:16:56: 7000000 INFO @ Tue, 16 Jun 2020 09:17:00: 3000000 INFO @ Tue, 16 Jun 2020 09:17:01: 8000000 INFO @ Tue, 16 Jun 2020 09:17:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:06: 4000000 INFO @ Tue, 16 Jun 2020 09:17:07: 9000000 INFO @ Tue, 16 Jun 2020 09:17:10: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:17:10: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:17:10: #1 total tags in treatment: 9552821 INFO @ Tue, 16 Jun 2020 09:17:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:10: #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 09:17:11: #1 tags after filtering in treatment: 9552821 INFO @ Tue, 16 Jun 2020 09:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:11: 5000000 INFO @ Tue, 16 Jun 2020 09:17:11: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 09:17:11: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:11: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:17:11: #2 alternative fragment length(s) may be 2,38,571,595 bps INFO @ Tue, 16 Jun 2020 09:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:11: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:11: #2 You may need to consider one of the other alternative d(s): 2,38,571,595 WARNING @ Tue, 16 Jun 2020 09:17:11: #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 09:17:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:16: 6000000 INFO @ Tue, 16 Jun 2020 09:17:22: 7000000 INFO @ Tue, 16 Jun 2020 09:17:27: 8000000 INFO @ Tue, 16 Jun 2020 09:17:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:32: 9000000 INFO @ Tue, 16 Jun 2020 09:17:35: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:17:35: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:17:35: #1 total tags in treatment: 9552821 INFO @ Tue, 16 Jun 2020 09:17:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:35: #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 09:17:35: #1 tags after filtering in treatment: 9552821 INFO @ Tue, 16 Jun 2020 09:17:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:35: #2 number of paired peaks: 282 WARNING @ Tue, 16 Jun 2020 09:17:35: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:35: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 09:17:35: #2 alternative fragment length(s) may be 2,38,571,595 bps INFO @ Tue, 16 Jun 2020 09:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:35: #2 You may need to consider one of the other alternative d(s): 2,38,571,595 WARNING @ Tue, 16 Jun 2020 09:17:35: #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 09:17:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495045/SRX495045.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 0 millis CompletedMACS2peakCalling