Job ID = 6368351 SRX = SRX495031 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:54 prefetch.2.10.7: 1) Downloading 'SRR1198563'... 2020-06-16T00:09:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:13:24 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:13:24 prefetch.2.10.7: 1) 'SRR1198563' was downloaded successfully Read 20667922 spots for SRR1198563/SRR1198563.sra Written 20667922 spots for SRR1198563/SRR1198563.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: 00:00:01 Multiseed full-index search: 00:04:24 20667922 reads; of these: 20667922 (100.00%) were unpaired; of these: 3294268 (15.94%) aligned 0 times 14825420 (71.73%) aligned exactly 1 time 2548234 (12.33%) aligned >1 times 84.06% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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] 1935767 / 17373654 = 0.1114 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 09:23:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.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 09:23:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:51: 1000000 INFO @ Tue, 16 Jun 2020 09:23:57: 2000000 INFO @ Tue, 16 Jun 2020 09:24:03: 3000000 INFO @ Tue, 16 Jun 2020 09:24:09: 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 09:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.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 09:24:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:15: 5000000 INFO @ Tue, 16 Jun 2020 09:24:20: 1000000 INFO @ Tue, 16 Jun 2020 09:24:21: 6000000 INFO @ Tue, 16 Jun 2020 09:24:26: 2000000 INFO @ Tue, 16 Jun 2020 09:24:27: 7000000 INFO @ Tue, 16 Jun 2020 09:24:32: 3000000 INFO @ Tue, 16 Jun 2020 09:24:33: 8000000 INFO @ Tue, 16 Jun 2020 09:24:37: 4000000 INFO @ Tue, 16 Jun 2020 09:24:39: 9000000 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 09:24:43: 5000000 INFO @ Tue, 16 Jun 2020 09:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.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 09:24:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:46: 10000000 INFO @ Tue, 16 Jun 2020 09:24:48: 6000000 INFO @ Tue, 16 Jun 2020 09:24:51: 1000000 INFO @ Tue, 16 Jun 2020 09:24:52: 11000000 INFO @ Tue, 16 Jun 2020 09:24:54: 7000000 INFO @ Tue, 16 Jun 2020 09:24:57: 2000000 INFO @ Tue, 16 Jun 2020 09:24:59: 12000000 INFO @ Tue, 16 Jun 2020 09:25:00: 8000000 INFO @ Tue, 16 Jun 2020 09:25:03: 3000000 INFO @ Tue, 16 Jun 2020 09:25:05: 13000000 INFO @ Tue, 16 Jun 2020 09:25:05: 9000000 INFO @ Tue, 16 Jun 2020 09:25:09: 4000000 INFO @ Tue, 16 Jun 2020 09:25:11: 10000000 INFO @ Tue, 16 Jun 2020 09:25:11: 14000000 INFO @ Tue, 16 Jun 2020 09:25:16: 5000000 INFO @ Tue, 16 Jun 2020 09:25:17: 11000000 INFO @ Tue, 16 Jun 2020 09:25:17: 15000000 INFO @ Tue, 16 Jun 2020 09:25:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:20: #1 total tags in treatment: 15437887 INFO @ Tue, 16 Jun 2020 09:25:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:20: #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 09:25:21: #1 tags after filtering in treatment: 15437887 INFO @ Tue, 16 Jun 2020 09:25:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:22: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 09:25:22: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:22: 6000000 INFO @ Tue, 16 Jun 2020 09:25:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:22: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:25:22: #2 alternative fragment length(s) may be 3,45,577,583 bps INFO @ Tue, 16 Jun 2020 09:25:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:22: #2 You may need to consider one of the other alternative d(s): 3,45,577,583 WARNING @ Tue, 16 Jun 2020 09:25:22: #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 09:25:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:23: 12000000 INFO @ Tue, 16 Jun 2020 09:25:28: 7000000 INFO @ Tue, 16 Jun 2020 09:25:28: 13000000 INFO @ Tue, 16 Jun 2020 09:25:34: 8000000 INFO @ Tue, 16 Jun 2020 09:25:34: 14000000 INFO @ Tue, 16 Jun 2020 09:25:39: 15000000 INFO @ Tue, 16 Jun 2020 09:25:40: 9000000 INFO @ Tue, 16 Jun 2020 09:25:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:42: #1 total tags in treatment: 15437887 INFO @ Tue, 16 Jun 2020 09:25:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:42: #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 09:25:42: #1 tags after filtering in treatment: 15437887 INFO @ Tue, 16 Jun 2020 09:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:43: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 09:25:43: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:43: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:25:43: #2 alternative fragment length(s) may be 3,45,577,583 bps INFO @ Tue, 16 Jun 2020 09:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.10_model.r WARNING @ Tue, 16 Jun 2020 09:25:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:43: #2 You may need to consider one of the other alternative d(s): 3,45,577,583 WARNING @ Tue, 16 Jun 2020 09:25:43: #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 09:25:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:46: 10000000 INFO @ Tue, 16 Jun 2020 09:25:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:52: 11000000 INFO @ Tue, 16 Jun 2020 09:25:58: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:04: 13000000 INFO @ Tue, 16 Jun 2020 09:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3395 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:10: 14000000 INFO @ Tue, 16 Jun 2020 09:26:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:16: 15000000 INFO @ Tue, 16 Jun 2020 09:26:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:19: #1 total tags in treatment: 15437887 INFO @ Tue, 16 Jun 2020 09:26:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:19: #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 09:26:19: #1 tags after filtering in treatment: 15437887 INFO @ Tue, 16 Jun 2020 09:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:20: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 09:26:20: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:21: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:26:21: #2 alternative fragment length(s) may be 3,45,577,583 bps INFO @ Tue, 16 Jun 2020 09:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:21: #2 You may need to consider one of the other alternative d(s): 3,45,577,583 WARNING @ Tue, 16 Jun 2020 09:26:21: #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 09:26:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (612 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495031/SRX495031.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling