Job ID = 6368097 SRX = SRX466560 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:53:18 prefetch.2.10.7: 1) Downloading 'SRR1163626'... 2020-06-15T23:53:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:04 prefetch.2.10.7: 1) 'SRR1163626' was downloaded successfully Read 21509609 spots for SRR1163626/SRR1163626.sra Written 21509609 spots for SRR1163626/SRR1163626.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: 00:03:57 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255393 (1.19%) aligned 0 times 17821489 (82.85%) aligned exactly 1 time 3432727 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 3667538 / 21254216 = 0.1726 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 09:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.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 09:07:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:10: 1000000 INFO @ Tue, 16 Jun 2020 09:07:16: 2000000 INFO @ Tue, 16 Jun 2020 09:07:21: 3000000 INFO @ Tue, 16 Jun 2020 09:07:26: 4000000 INFO @ Tue, 16 Jun 2020 09:07:32: 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 09:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.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 09:07:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:37: 6000000 INFO @ Tue, 16 Jun 2020 09:07:41: 1000000 INFO @ Tue, 16 Jun 2020 09:07:43: 7000000 INFO @ Tue, 16 Jun 2020 09:07:46: 2000000 INFO @ Tue, 16 Jun 2020 09:07:48: 8000000 INFO @ Tue, 16 Jun 2020 09:07:51: 3000000 INFO @ Tue, 16 Jun 2020 09:07:53: 9000000 INFO @ Tue, 16 Jun 2020 09:07:57: 4000000 INFO @ Tue, 16 Jun 2020 09:07:59: 10000000 INFO @ Tue, 16 Jun 2020 09:08:02: 5000000 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 09:08:04: 11000000 INFO @ Tue, 16 Jun 2020 09:08:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.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 09:08:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:07: 6000000 INFO @ Tue, 16 Jun 2020 09:08:10: 12000000 INFO @ Tue, 16 Jun 2020 09:08:10: 1000000 INFO @ Tue, 16 Jun 2020 09:08:13: 7000000 INFO @ Tue, 16 Jun 2020 09:08:15: 2000000 INFO @ Tue, 16 Jun 2020 09:08:15: 13000000 INFO @ Tue, 16 Jun 2020 09:08:18: 8000000 INFO @ Tue, 16 Jun 2020 09:08:20: 3000000 INFO @ Tue, 16 Jun 2020 09:08:21: 14000000 INFO @ Tue, 16 Jun 2020 09:08:24: 9000000 INFO @ Tue, 16 Jun 2020 09:08:24: 4000000 INFO @ Tue, 16 Jun 2020 09:08:27: 15000000 INFO @ Tue, 16 Jun 2020 09:08:29: 5000000 INFO @ Tue, 16 Jun 2020 09:08:29: 10000000 INFO @ Tue, 16 Jun 2020 09:08:32: 16000000 INFO @ Tue, 16 Jun 2020 09:08:34: 6000000 INFO @ Tue, 16 Jun 2020 09:08:35: 11000000 INFO @ Tue, 16 Jun 2020 09:08:38: 17000000 INFO @ Tue, 16 Jun 2020 09:08:39: 7000000 INFO @ Tue, 16 Jun 2020 09:08:40: 12000000 INFO @ Tue, 16 Jun 2020 09:08:41: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:08:41: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:08:41: #1 total tags in treatment: 17586678 INFO @ Tue, 16 Jun 2020 09:08:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:41: #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 09:08:42: #1 tags after filtering in treatment: 17586678 INFO @ Tue, 16 Jun 2020 09:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:43: #2 number of paired peaks: 215 WARNING @ Tue, 16 Jun 2020 09:08:43: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:43: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:08:43: #2 alternative fragment length(s) may be 1,39,95,592 bps INFO @ Tue, 16 Jun 2020 09:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.05_model.r WARNING @ Tue, 16 Jun 2020 09:08:43: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:43: #2 You may need to consider one of the other alternative d(s): 1,39,95,592 WARNING @ Tue, 16 Jun 2020 09:08:43: #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 09:08:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:44: 8000000 INFO @ Tue, 16 Jun 2020 09:08:46: 13000000 INFO @ Tue, 16 Jun 2020 09:08:48: 9000000 INFO @ Tue, 16 Jun 2020 09:08:51: 14000000 INFO @ Tue, 16 Jun 2020 09:08:53: 10000000 INFO @ Tue, 16 Jun 2020 09:08:57: 15000000 INFO @ Tue, 16 Jun 2020 09:08:58: 11000000 INFO @ Tue, 16 Jun 2020 09:09:02: 16000000 INFO @ Tue, 16 Jun 2020 09:09:03: 12000000 INFO @ Tue, 16 Jun 2020 09:09:08: 13000000 INFO @ Tue, 16 Jun 2020 09:09:08: 17000000 INFO @ Tue, 16 Jun 2020 09:09:11: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:09:11: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:09:11: #1 total tags in treatment: 17586678 INFO @ Tue, 16 Jun 2020 09:09:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:11: #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 09:09:12: #1 tags after filtering in treatment: 17586678 INFO @ Tue, 16 Jun 2020 09:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:12: 14000000 INFO @ Tue, 16 Jun 2020 09:09:13: #2 number of paired peaks: 215 WARNING @ Tue, 16 Jun 2020 09:09:13: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:13: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:09:13: #2 alternative fragment length(s) may be 1,39,95,592 bps INFO @ Tue, 16 Jun 2020 09:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.10_model.r WARNING @ Tue, 16 Jun 2020 09:09:13: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:13: #2 You may need to consider one of the other alternative d(s): 1,39,95,592 WARNING @ Tue, 16 Jun 2020 09:09:13: #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 09:09:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:17: 15000000 INFO @ Tue, 16 Jun 2020 09:09:22: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:09:27: 17000000 INFO @ Tue, 16 Jun 2020 09:09:30: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:09:30: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:09:30: #1 total tags in treatment: 17586678 INFO @ Tue, 16 Jun 2020 09:09:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:30: #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 09:09:30: #1 tags after filtering in treatment: 17586678 INFO @ Tue, 16 Jun 2020 09:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:31: #2 number of paired peaks: 215 WARNING @ Tue, 16 Jun 2020 09:09:31: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:31: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:09:31: #2 alternative fragment length(s) may be 1,39,95,592 bps INFO @ Tue, 16 Jun 2020 09:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:31: #2 You may need to consider one of the other alternative d(s): 1,39,95,592 WARNING @ Tue, 16 Jun 2020 09:09:31: #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 09:09:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.10_summits.bed INFO @ Tue, 16 Jun 2020 09:09:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (340 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:10:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466560/SRX466560.20_summits.bed INFO @ Tue, 16 Jun 2020 09:10:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling