Job ID = 6368956 SRX = SRX7627596 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:45 prefetch.2.10.7: 1) Downloading 'SRR10961946'... 2020-06-16T00:30:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:22 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:23 prefetch.2.10.7: 'SRR10961946' is valid 2020-06-16T00:32:23 prefetch.2.10.7: 1) 'SRR10961946' was downloaded successfully Read 13561672 spots for SRR10961946/SRR10961946.sra Written 13561672 spots for SRR10961946/SRR10961946.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: 00:03:18 13561672 reads; of these: 13561672 (100.00%) were unpaired; of these: 658753 (4.86%) aligned 0 times 10788213 (79.55%) aligned exactly 1 time 2114706 (15.59%) aligned >1 times 95.14% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 3542481 / 12902919 = 0.2745 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 09:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.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 09:40:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:13: 1000000 INFO @ Tue, 16 Jun 2020 09:40:20: 2000000 INFO @ Tue, 16 Jun 2020 09:40:27: 3000000 INFO @ Tue, 16 Jun 2020 09:40:34: 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 09:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.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 09:40:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:41: 5000000 INFO @ Tue, 16 Jun 2020 09:40:43: 1000000 INFO @ Tue, 16 Jun 2020 09:40:48: 6000000 INFO @ Tue, 16 Jun 2020 09:40:51: 2000000 INFO @ Tue, 16 Jun 2020 09:40:56: 7000000 INFO @ Tue, 16 Jun 2020 09:40:58: 3000000 INFO @ Tue, 16 Jun 2020 09:41:03: 8000000 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 09:41:05: 4000000 INFO @ Tue, 16 Jun 2020 09:41:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.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 09:41:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:11: 9000000 INFO @ Tue, 16 Jun 2020 09:41:13: 1000000 INFO @ Tue, 16 Jun 2020 09:41:13: 5000000 INFO @ Tue, 16 Jun 2020 09:41:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:13: #1 total tags in treatment: 9360438 INFO @ Tue, 16 Jun 2020 09:41:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:13: #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 09:41:13: #1 tags after filtering in treatment: 9360438 INFO @ Tue, 16 Jun 2020 09:41:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:14: #2 number of paired peaks: 407 WARNING @ Tue, 16 Jun 2020 09:41:14: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:14: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:14: #2 alternative fragment length(s) may be 3,48,576 bps INFO @ Tue, 16 Jun 2020 09:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:14: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:14: #2 You may need to consider one of the other alternative d(s): 3,48,576 WARNING @ Tue, 16 Jun 2020 09:41:14: #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 09:41:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:19: 2000000 INFO @ Tue, 16 Jun 2020 09:41:20: 6000000 INFO @ Tue, 16 Jun 2020 09:41:26: 3000000 INFO @ Tue, 16 Jun 2020 09:41:28: 7000000 INFO @ Tue, 16 Jun 2020 09:41:33: 4000000 INFO @ Tue, 16 Jun 2020 09:41:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:35: 8000000 INFO @ Tue, 16 Jun 2020 09:41:39: 5000000 INFO @ Tue, 16 Jun 2020 09:41:43: 9000000 INFO @ Tue, 16 Jun 2020 09:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (713 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:45: #1 total tags in treatment: 9360438 INFO @ Tue, 16 Jun 2020 09:41:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:45: #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 09:41:45: #1 tags after filtering in treatment: 9360438 INFO @ Tue, 16 Jun 2020 09:41:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:46: 6000000 INFO @ Tue, 16 Jun 2020 09:41:46: #2 number of paired peaks: 407 WARNING @ Tue, 16 Jun 2020 09:41:46: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:46: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:46: #2 alternative fragment length(s) may be 3,48,576 bps INFO @ Tue, 16 Jun 2020 09:41:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:46: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:46: #2 You may need to consider one of the other alternative d(s): 3,48,576 WARNING @ Tue, 16 Jun 2020 09:41:46: #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 09:41:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:52: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:58: 8000000 INFO @ Tue, 16 Jun 2020 09:42:04: 9000000 INFO @ Tue, 16 Jun 2020 09:42:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:07: #1 total tags in treatment: 9360438 INFO @ Tue, 16 Jun 2020 09:42:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:07: #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 09:42:07: #1 tags after filtering in treatment: 9360438 INFO @ Tue, 16 Jun 2020 09:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:07: #2 number of paired peaks: 407 WARNING @ Tue, 16 Jun 2020 09:42:07: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:08: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:42:08: #2 alternative fragment length(s) may be 3,48,576 bps INFO @ Tue, 16 Jun 2020 09:42:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:08: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:08: #2 You may need to consider one of the other alternative d(s): 3,48,576 WARNING @ Tue, 16 Jun 2020 09:42:08: #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 09:42:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627596/SRX7627596.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling