Job ID = 6368063 SRX = SRX466526 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:42:14 prefetch.2.10.7: 1) Downloading 'SRR1163592'... 2020-06-15T23:42:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:19 prefetch.2.10.7: 1) 'SRR1163592' was downloaded successfully Read 13375373 spots for SRR1163592/SRR1163592.sra Written 13375373 spots for SRR1163592/SRR1163592.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: 00:02:22 13375373 reads; of these: 13375373 (100.00%) were unpaired; of these: 2346164 (17.54%) aligned 0 times 8809257 (65.86%) aligned exactly 1 time 2219952 (16.60%) aligned >1 times 82.46% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 4094011 / 11029209 = 0.3712 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 08:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.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 08:55:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:56: 1000000 INFO @ Tue, 16 Jun 2020 08:56:03: 2000000 INFO @ Tue, 16 Jun 2020 08:56:10: 3000000 INFO @ Tue, 16 Jun 2020 08:56:16: 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 08:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.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 08:56:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:23: 5000000 INFO @ Tue, 16 Jun 2020 08:56:27: 1000000 INFO @ Tue, 16 Jun 2020 08:56:30: 6000000 INFO @ Tue, 16 Jun 2020 08:56:34: 2000000 INFO @ Tue, 16 Jun 2020 08:56:36: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:56:36: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:56:36: #1 total tags in treatment: 6935198 INFO @ Tue, 16 Jun 2020 08:56:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:36: #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 08:56:37: #1 tags after filtering in treatment: 6935198 INFO @ Tue, 16 Jun 2020 08:56:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:37: #2 number of paired peaks: 491 WARNING @ Tue, 16 Jun 2020 08:56:37: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:37: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:56:37: #2 alternative fragment length(s) may be 2,41,549,588 bps INFO @ Tue, 16 Jun 2020 08:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.05_model.r WARNING @ Tue, 16 Jun 2020 08:56:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:37: #2 You may need to consider one of the other alternative d(s): 2,41,549,588 WARNING @ Tue, 16 Jun 2020 08:56:37: #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 08:56:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:41: 3000000 INFO @ Tue, 16 Jun 2020 08:56:47: 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 08:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.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 08:56:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:54: 5000000 INFO @ Tue, 16 Jun 2020 08:56:57: 1000000 INFO @ Tue, 16 Jun 2020 08:56:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.05_summits.bed INFO @ Tue, 16 Jun 2020 08:56:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (794 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:01: 6000000 INFO @ Tue, 16 Jun 2020 08:57:04: 2000000 INFO @ Tue, 16 Jun 2020 08:57:07: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:57:07: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:57:07: #1 total tags in treatment: 6935198 INFO @ Tue, 16 Jun 2020 08:57:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:07: #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 08:57:07: #1 tags after filtering in treatment: 6935198 INFO @ Tue, 16 Jun 2020 08:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:08: #2 number of paired peaks: 491 WARNING @ Tue, 16 Jun 2020 08:57:08: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:08: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:57:08: #2 alternative fragment length(s) may be 2,41,549,588 bps INFO @ Tue, 16 Jun 2020 08:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.10_model.r WARNING @ Tue, 16 Jun 2020 08:57:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:08: #2 You may need to consider one of the other alternative d(s): 2,41,549,588 WARNING @ Tue, 16 Jun 2020 08:57:08: #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 08:57:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:11: 3000000 INFO @ Tue, 16 Jun 2020 08:57:18: 4000000 INFO @ Tue, 16 Jun 2020 08:57:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:26: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.10_summits.bed INFO @ Tue, 16 Jun 2020 08:57:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:32: 6000000 INFO @ Tue, 16 Jun 2020 08:57:39: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:57:39: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:57:39: #1 total tags in treatment: 6935198 INFO @ Tue, 16 Jun 2020 08:57:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:39: #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 08:57:39: #1 tags after filtering in treatment: 6935198 INFO @ Tue, 16 Jun 2020 08:57:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:39: #2 number of paired peaks: 491 WARNING @ Tue, 16 Jun 2020 08:57:39: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:40: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:57:40: #2 alternative fragment length(s) may be 2,41,549,588 bps INFO @ Tue, 16 Jun 2020 08:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.20_model.r WARNING @ Tue, 16 Jun 2020 08:57:40: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:40: #2 You may need to consider one of the other alternative d(s): 2,41,549,588 WARNING @ Tue, 16 Jun 2020 08:57:40: #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 08:57:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466526/SRX466526.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling