Job ID = 6367434 SRX = SRX331192 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:01 prefetch.2.10.7: 1) Downloading 'SRR947424'... 2020-06-15T23:25:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:32 prefetch.2.10.7: 'SRR947424' is valid 2020-06-15T23:25:32 prefetch.2.10.7: 1) 'SRR947424' was downloaded successfully Read 7337628 spots for SRR947424/SRR947424.sra Written 7337628 spots for SRR947424/SRR947424.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: 00:01:13 7337628 reads; of these: 7337628 (100.00%) were unpaired; of these: 420893 (5.74%) aligned 0 times 5798736 (79.03%) aligned exactly 1 time 1117999 (15.24%) aligned >1 times 94.26% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 976662 / 6916735 = 0.1412 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 08:28:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.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 08:28:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:00: 1000000 INFO @ Tue, 16 Jun 2020 08:29:06: 2000000 INFO @ Tue, 16 Jun 2020 08:29:13: 3000000 INFO @ Tue, 16 Jun 2020 08:29:19: 4000000 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 08:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.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 08:29:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:26: 5000000 INFO @ Tue, 16 Jun 2020 08:29:31: 1000000 INFO @ Tue, 16 Jun 2020 08:29:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:32: #1 total tags in treatment: 5940073 INFO @ Tue, 16 Jun 2020 08:29:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:32: #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 08:29:32: #1 tags after filtering in treatment: 5940073 INFO @ Tue, 16 Jun 2020 08:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:33: #2 number of paired peaks: 464 WARNING @ Tue, 16 Jun 2020 08:29:33: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:33: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:29:33: #2 alternative fragment length(s) may be 2,31,526,551,592 bps INFO @ Tue, 16 Jun 2020 08:29:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.05_model.r WARNING @ Tue, 16 Jun 2020 08:29:33: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:33: #2 You may need to consider one of the other alternative d(s): 2,31,526,551,592 WARNING @ Tue, 16 Jun 2020 08:29:33: #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 08:29:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:37: 2000000 INFO @ Tue, 16 Jun 2020 08:29:44: 3000000 INFO @ Tue, 16 Jun 2020 08:29:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:51: 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 08:29:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.05_summits.bed INFO @ Tue, 16 Jun 2020 08:29:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.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 08:29:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:59: 5000000 INFO @ Tue, 16 Jun 2020 08:30:01: 1000000 INFO @ Tue, 16 Jun 2020 08:30:06: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:06: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:06: #1 total tags in treatment: 5940073 INFO @ Tue, 16 Jun 2020 08:30:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:06: #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 08:30:06: #1 tags after filtering in treatment: 5940073 INFO @ Tue, 16 Jun 2020 08:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:06: #2 number of paired peaks: 464 WARNING @ Tue, 16 Jun 2020 08:30:06: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:06: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:30:06: #2 alternative fragment length(s) may be 2,31,526,551,592 bps INFO @ Tue, 16 Jun 2020 08:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:06: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:06: #2 You may need to consider one of the other alternative d(s): 2,31,526,551,592 WARNING @ Tue, 16 Jun 2020 08:30:06: #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 08:30:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:09: 2000000 INFO @ Tue, 16 Jun 2020 08:30:15: 3000000 INFO @ Tue, 16 Jun 2020 08:30:19: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:30:22: 4000000 INFO @ Tue, 16 Jun 2020 08:30:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.10_summits.bed INFO @ Tue, 16 Jun 2020 08:30:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:29: 5000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:30:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:35: #1 total tags in treatment: 5940073 INFO @ Tue, 16 Jun 2020 08:30:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:35: #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 08:30:35: #1 tags after filtering in treatment: 5940073 INFO @ Tue, 16 Jun 2020 08:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:36: #2 number of paired peaks: 464 WARNING @ Tue, 16 Jun 2020 08:30:36: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:36: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:30:36: #2 alternative fragment length(s) may be 2,31,526,551,592 bps INFO @ Tue, 16 Jun 2020 08:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.20_model.r WARNING @ Tue, 16 Jun 2020 08:30:36: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:36: #2 You may need to consider one of the other alternative d(s): 2,31,526,551,592 WARNING @ Tue, 16 Jun 2020 08:30:36: #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 08:30:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331192/SRX331192.20_summits.bed INFO @ Tue, 16 Jun 2020 08:30:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (69 records, 4 fields): 1 millis CompletedMACS2peakCalling