Job ID = 6367733 SRX = SRX4082347 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:39:29 prefetch.2.10.7: 1) Downloading 'SRR7164165'... 2020-06-15T23:39:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:23 prefetch.2.10.7: 'SRR7164165' is valid 2020-06-15T23:41:23 prefetch.2.10.7: 1) 'SRR7164165' was downloaded successfully 2020-06-15T23:41:23 prefetch.2.10.7: 'SRR7164165' has 0 unresolved dependencies Read 13936847 spots for SRR7164165/SRR7164165.sra Written 13936847 spots for SRR7164165/SRR7164165.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: 00:03:07 13936847 reads; of these: 13936847 (100.00%) were unpaired; of these: 84432 (0.61%) aligned 0 times 12031701 (86.33%) aligned exactly 1 time 1820714 (13.06%) aligned >1 times 99.39% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 1417755 / 13852415 = 0.1023 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 08:48:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.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 08:48:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:56: 1000000 INFO @ Tue, 16 Jun 2020 08:49:02: 2000000 INFO @ Tue, 16 Jun 2020 08:49:08: 3000000 INFO @ Tue, 16 Jun 2020 08:49:14: 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 08:49:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.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 08:49:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:20: 5000000 INFO @ Tue, 16 Jun 2020 08:49:26: 1000000 INFO @ Tue, 16 Jun 2020 08:49:27: 6000000 INFO @ Tue, 16 Jun 2020 08:49:33: 2000000 INFO @ Tue, 16 Jun 2020 08:49:34: 7000000 INFO @ Tue, 16 Jun 2020 08:49:39: 3000000 INFO @ Tue, 16 Jun 2020 08:49:40: 8000000 INFO @ Tue, 16 Jun 2020 08:49:46: 4000000 INFO @ Tue, 16 Jun 2020 08:49:47: 9000000 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 08:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.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 08:49:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:53: 5000000 INFO @ Tue, 16 Jun 2020 08:49:54: 10000000 INFO @ Tue, 16 Jun 2020 08:49:56: 1000000 INFO @ Tue, 16 Jun 2020 08:49:59: 6000000 INFO @ Tue, 16 Jun 2020 08:50:01: 11000000 INFO @ Tue, 16 Jun 2020 08:50:03: 2000000 INFO @ Tue, 16 Jun 2020 08:50:06: 7000000 INFO @ Tue, 16 Jun 2020 08:50:08: 12000000 INFO @ Tue, 16 Jun 2020 08:50:09: 3000000 INFO @ Tue, 16 Jun 2020 08:50:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:10: #1 total tags in treatment: 12434660 INFO @ Tue, 16 Jun 2020 08:50:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:10: #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 08:50:11: #1 tags after filtering in treatment: 12434660 INFO @ Tue, 16 Jun 2020 08:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:12: #2 number of paired peaks: 129 WARNING @ Tue, 16 Jun 2020 08:50:12: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:12: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:50:12: #2 alternative fragment length(s) may be 3,47,507,567,592 bps INFO @ Tue, 16 Jun 2020 08:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:12: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:12: #2 You may need to consider one of the other alternative d(s): 3,47,507,567,592 WARNING @ Tue, 16 Jun 2020 08:50:12: #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 08:50:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:12: 8000000 INFO @ Tue, 16 Jun 2020 08:50:16: 4000000 INFO @ Tue, 16 Jun 2020 08:50:19: 9000000 INFO @ Tue, 16 Jun 2020 08:50:22: 5000000 INFO @ Tue, 16 Jun 2020 08:50:25: 10000000 INFO @ Tue, 16 Jun 2020 08:50:29: 6000000 INFO @ Tue, 16 Jun 2020 08:50:32: 11000000 INFO @ Tue, 16 Jun 2020 08:50:35: 7000000 INFO @ Tue, 16 Jun 2020 08:50:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:38: 12000000 INFO @ Tue, 16 Jun 2020 08:50:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:41: #1 total tags in treatment: 12434660 INFO @ Tue, 16 Jun 2020 08:50:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:41: #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 08:50:41: #1 tags after filtering in treatment: 12434660 INFO @ Tue, 16 Jun 2020 08:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:42: 8000000 INFO @ Tue, 16 Jun 2020 08:50:42: #2 number of paired peaks: 129 WARNING @ Tue, 16 Jun 2020 08:50:42: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:42: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:50:42: #2 alternative fragment length(s) may be 3,47,507,567,592 bps INFO @ Tue, 16 Jun 2020 08:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:42: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:42: #2 You may need to consider one of the other alternative d(s): 3,47,507,567,592 WARNING @ Tue, 16 Jun 2020 08:50:42: #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 08:50:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:48: 9000000 INFO @ Tue, 16 Jun 2020 08:50:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:53: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:59: 11000000 INFO @ Tue, 16 Jun 2020 08:51:05: 12000000 INFO @ Tue, 16 Jun 2020 08:51:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:08: #1 total tags in treatment: 12434660 INFO @ Tue, 16 Jun 2020 08:51:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:08: #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 08:51:08: #1 tags after filtering in treatment: 12434660 INFO @ Tue, 16 Jun 2020 08:51:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:09: #2 number of paired peaks: 129 WARNING @ Tue, 16 Jun 2020 08:51:09: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:09: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:51:09: #2 alternative fragment length(s) may be 3,47,507,567,592 bps INFO @ Tue, 16 Jun 2020 08:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:09: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:09: #2 You may need to consider one of the other alternative d(s): 3,47,507,567,592 WARNING @ Tue, 16 Jun 2020 08:51:09: #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 08:51:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082347/SRX4082347.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 1 millis CompletedMACS2peakCalling