Job ID = 6367690 SRX = SRX3942553 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:20 prefetch.2.10.7: 1) Downloading 'SRR7010074'... 2020-06-15T23:30:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:07 prefetch.2.10.7: 'SRR7010074' is valid 2020-06-15T23:32:07 prefetch.2.10.7: 1) 'SRR7010074' was downloaded successfully 2020-06-15T23:32:07 prefetch.2.10.7: 'SRR7010074' has 0 unresolved dependencies Read 16348560 spots for SRR7010074/SRR7010074.sra Written 16348560 spots for SRR7010074/SRR7010074.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: 00:05:33 16348560 reads; of these: 16348560 (100.00%) were unpaired; of these: 2869378 (17.55%) aligned 0 times 10224263 (62.54%) aligned exactly 1 time 3254919 (19.91%) aligned >1 times 82.45% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 6377141 / 13479182 = 0.4731 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 08:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.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 08:41:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:55: 1000000 INFO @ Tue, 16 Jun 2020 08:42:01: 2000000 INFO @ Tue, 16 Jun 2020 08:42:06: 3000000 INFO @ Tue, 16 Jun 2020 08:42:11: 4000000 INFO @ Tue, 16 Jun 2020 08:42:17: 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 08:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.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 08:42:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:22: 6000000 INFO @ Tue, 16 Jun 2020 08:42:27: 1000000 INFO @ Tue, 16 Jun 2020 08:42:28: 7000000 INFO @ Tue, 16 Jun 2020 08:42:29: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:42:29: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:42:29: #1 total tags in treatment: 7102041 INFO @ Tue, 16 Jun 2020 08:42:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:29: #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 08:42:29: #1 tags after filtering in treatment: 7102041 INFO @ Tue, 16 Jun 2020 08:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:30: #2 number of paired peaks: 1594 INFO @ Tue, 16 Jun 2020 08:42:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:30: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 08:42:30: #2 alternative fragment length(s) may be 2,83 bps INFO @ Tue, 16 Jun 2020 08:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.05_model.r WARNING @ Tue, 16 Jun 2020 08:42:30: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:30: #2 You may need to consider one of the other alternative d(s): 2,83 WARNING @ Tue, 16 Jun 2020 08:42:30: #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 08:42:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:34: 2000000 INFO @ Tue, 16 Jun 2020 08:42:40: 3000000 INFO @ Tue, 16 Jun 2020 08:42:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:47: 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 08:42:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.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 08:42:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1078 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:54: 5000000 INFO @ Tue, 16 Jun 2020 08:42:57: 1000000 INFO @ Tue, 16 Jun 2020 08:43:01: 6000000 INFO @ Tue, 16 Jun 2020 08:43:03: 2000000 INFO @ Tue, 16 Jun 2020 08:43:08: 7000000 INFO @ Tue, 16 Jun 2020 08:43:09: 3000000 INFO @ Tue, 16 Jun 2020 08:43:09: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:43:09: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:43:09: #1 total tags in treatment: 7102041 INFO @ Tue, 16 Jun 2020 08:43:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:09: #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 08:43:09: #1 tags after filtering in treatment: 7102041 INFO @ Tue, 16 Jun 2020 08:43:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:09: #2 number of paired peaks: 1594 INFO @ Tue, 16 Jun 2020 08:43:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:09: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 08:43:09: #2 alternative fragment length(s) may be 2,83 bps INFO @ Tue, 16 Jun 2020 08:43:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.10_model.r WARNING @ Tue, 16 Jun 2020 08:43:09: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:09: #2 You may need to consider one of the other alternative d(s): 2,83 WARNING @ Tue, 16 Jun 2020 08:43:09: #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 08:43:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:14: 4000000 INFO @ Tue, 16 Jun 2020 08:43:20: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:25: 6000000 INFO @ Tue, 16 Jun 2020 08:43:31: 7000000 INFO @ Tue, 16 Jun 2020 08:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.10_summits.bed INFO @ Tue, 16 Jun 2020 08:43:31: Done! INFO @ Tue, 16 Jun 2020 08:43:31: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:43:31: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:43:31: #1 total tags in treatment: 7102041 INFO @ Tue, 16 Jun 2020 08:43:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (486 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:31: #1 tags after filtering in treatment: 7102041 INFO @ Tue, 16 Jun 2020 08:43:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:32: #2 number of paired peaks: 1594 INFO @ Tue, 16 Jun 2020 08:43:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:32: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 08:43:32: #2 alternative fragment length(s) may be 2,83 bps INFO @ Tue, 16 Jun 2020 08:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.20_model.r WARNING @ Tue, 16 Jun 2020 08:43:32: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:32: #2 You may need to consider one of the other alternative d(s): 2,83 WARNING @ Tue, 16 Jun 2020 08:43:32: #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 08:43:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:43:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942553/SRX3942553.20_summits.bed INFO @ Tue, 16 Jun 2020 08:43:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (243 records, 4 fields): 1 millis CompletedMACS2peakCalling