Job ID = 6368968 SRX = SRX7971794 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:17 prefetch.2.10.7: 1) Downloading 'SRR11392680'... 2020-06-16T00:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:43 prefetch.2.10.7: 1) 'SRR11392680' was downloaded successfully Read 21768229 spots for SRR11392680/SRR11392680.sra Written 21768229 spots for SRR11392680/SRR11392680.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: 00:07:44 21768229 reads; of these: 21768229 (100.00%) were unpaired; of these: 805394 (3.70%) aligned 0 times 16115403 (74.03%) aligned exactly 1 time 4847432 (22.27%) aligned >1 times 96.30% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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 12 files... [bam_rmdupse_core] 3817551 / 20962835 = 0.1821 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 10:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.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 10:03:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:03:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:03:52: 1000000 INFO @ Tue, 16 Jun 2020 10:03:59: 2000000 INFO @ Tue, 16 Jun 2020 10:04:06: 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 10:04:13: 4000000 INFO @ Tue, 16 Jun 2020 10:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.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 10:04:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:21: 5000000 INFO @ Tue, 16 Jun 2020 10:04:21: 1000000 INFO @ Tue, 16 Jun 2020 10:04:28: 2000000 INFO @ Tue, 16 Jun 2020 10:04:28: 6000000 INFO @ Tue, 16 Jun 2020 10:04:35: 3000000 INFO @ Tue, 16 Jun 2020 10:04:36: 7000000 INFO @ Tue, 16 Jun 2020 10:04:41: 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 10:04:43: 8000000 INFO @ Tue, 16 Jun 2020 10:04:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.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 10:04:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:48: 5000000 INFO @ Tue, 16 Jun 2020 10:04:50: 9000000 INFO @ Tue, 16 Jun 2020 10:04:52: 1000000 INFO @ Tue, 16 Jun 2020 10:04:55: 6000000 INFO @ Tue, 16 Jun 2020 10:04:58: 10000000 INFO @ Tue, 16 Jun 2020 10:05:00: 2000000 INFO @ Tue, 16 Jun 2020 10:05:02: 7000000 INFO @ Tue, 16 Jun 2020 10:05:05: 11000000 INFO @ Tue, 16 Jun 2020 10:05:07: 3000000 INFO @ Tue, 16 Jun 2020 10:05:08: 8000000 INFO @ Tue, 16 Jun 2020 10:05:13: 12000000 INFO @ Tue, 16 Jun 2020 10:05:15: 4000000 INFO @ Tue, 16 Jun 2020 10:05:15: 9000000 INFO @ Tue, 16 Jun 2020 10:05:20: 13000000 INFO @ Tue, 16 Jun 2020 10:05:22: 5000000 INFO @ Tue, 16 Jun 2020 10:05:22: 10000000 INFO @ Tue, 16 Jun 2020 10:05:28: 14000000 INFO @ Tue, 16 Jun 2020 10:05:29: 11000000 INFO @ Tue, 16 Jun 2020 10:05:29: 6000000 INFO @ Tue, 16 Jun 2020 10:05:35: 15000000 INFO @ Tue, 16 Jun 2020 10:05:36: 12000000 INFO @ Tue, 16 Jun 2020 10:05:37: 7000000 INFO @ Tue, 16 Jun 2020 10:05:42: 13000000 INFO @ Tue, 16 Jun 2020 10:05:43: 16000000 INFO @ Tue, 16 Jun 2020 10:05:44: 8000000 INFO @ Tue, 16 Jun 2020 10:05:49: 14000000 INFO @ Tue, 16 Jun 2020 10:05:50: 17000000 INFO @ Tue, 16 Jun 2020 10:05:51: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:05:51: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:05:51: #1 total tags in treatment: 17145284 INFO @ Tue, 16 Jun 2020 10:05:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:51: #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 10:05:52: #1 tags after filtering in treatment: 17145284 INFO @ Tue, 16 Jun 2020 10:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:05:52: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:52: 9000000 INFO @ Tue, 16 Jun 2020 10:05:53: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 10:05:53: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:53: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:53: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:53: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:53: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:53: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 10:05:53: #2 alternative fragment length(s) may be 2,51,57,63,567,573 bps INFO @ Tue, 16 Jun 2020 10:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.05_model.r WARNING @ Tue, 16 Jun 2020 10:05:53: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:05:53: #2 You may need to consider one of the other alternative d(s): 2,51,57,63,567,573 WARNING @ Tue, 16 Jun 2020 10:05:53: #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 10:05:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:56: 15000000 INFO @ Tue, 16 Jun 2020 10:05:59: 10000000 INFO @ Tue, 16 Jun 2020 10:06:03: 16000000 INFO @ Tue, 16 Jun 2020 10:06:06: 11000000 INFO @ Tue, 16 Jun 2020 10:06:10: 17000000 INFO @ Tue, 16 Jun 2020 10:06:11: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:06:11: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:06:11: #1 total tags in treatment: 17145284 INFO @ Tue, 16 Jun 2020 10:06:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:11: #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 10:06:11: #1 tags after filtering in treatment: 17145284 INFO @ Tue, 16 Jun 2020 10:06:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:06:11: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:12: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 10:06:12: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 10:06:12: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:13: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:13: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:13: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:13: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 10:06:13: #2 alternative fragment length(s) may be 2,51,57,63,567,573 bps INFO @ Tue, 16 Jun 2020 10:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.10_model.r WARNING @ Tue, 16 Jun 2020 10:06:13: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:06:13: #2 You may need to consider one of the other alternative d(s): 2,51,57,63,567,573 WARNING @ Tue, 16 Jun 2020 10:06:13: #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 10:06:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:06:14: 12000000 INFO @ Tue, 16 Jun 2020 10:06:21: 13000000 INFO @ Tue, 16 Jun 2020 10:06:28: 14000000 INFO @ Tue, 16 Jun 2020 10:06:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:06:35: 15000000 INFO @ Tue, 16 Jun 2020 10:06:42: 16000000 INFO @ Tue, 16 Jun 2020 10:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.05_summits.bed INFO @ Tue, 16 Jun 2020 10:06:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1708 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:06:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:06:50: 17000000 INFO @ Tue, 16 Jun 2020 10:06:51: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:06:51: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:06:51: #1 total tags in treatment: 17145284 INFO @ Tue, 16 Jun 2020 10:06:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:51: #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 10:06:51: #1 tags after filtering in treatment: 17145284 INFO @ Tue, 16 Jun 2020 10:06:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:06:51: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:52: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 10:06:52: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 10:06:52: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:52: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:52: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:52: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:52: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 10:06:52: #2 alternative fragment length(s) may be 2,51,57,63,567,573 bps INFO @ Tue, 16 Jun 2020 10:06:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.20_model.r WARNING @ Tue, 16 Jun 2020 10:06:52: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:06:52: #2 You may need to consider one of the other alternative d(s): 2,51,57,63,567,573 WARNING @ Tue, 16 Jun 2020 10:06:52: #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 10:06:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:07:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.10_summits.bed INFO @ Tue, 16 Jun 2020 10:07:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (646 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:07:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971794/SRX7971794.20_summits.bed INFO @ Tue, 16 Jun 2020 10:07:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 1 millis CompletedMACS2peakCalling