Job ID = 6368360 SRX = SRX495040 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:05 prefetch.2.10.7: 1) Downloading 'SRR1198572'... 2020-06-16T00:14:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:18:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:18:58 prefetch.2.10.7: 1) 'SRR1198572' was downloaded successfully Read 23628764 spots for SRR1198572/SRR1198572.sra Written 23628764 spots for SRR1198572/SRR1198572.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: 00:04:54 23628764 reads; of these: 23628764 (100.00%) were unpaired; of these: 7049148 (29.83%) aligned 0 times 12298576 (52.05%) aligned exactly 1 time 4281040 (18.12%) aligned >1 times 70.17% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 7153693 / 16579616 = 0.4315 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 09:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.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 09:29:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:09: 1000000 INFO @ Tue, 16 Jun 2020 09:29:15: 2000000 INFO @ Tue, 16 Jun 2020 09:29:20: 3000000 INFO @ Tue, 16 Jun 2020 09:29:26: 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 09:29:32: 5000000 INFO @ Tue, 16 Jun 2020 09:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.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 09:29:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:37: 6000000 INFO @ Tue, 16 Jun 2020 09:29:39: 1000000 INFO @ Tue, 16 Jun 2020 09:29:43: 7000000 INFO @ Tue, 16 Jun 2020 09:29:44: 2000000 INFO @ Tue, 16 Jun 2020 09:29:49: 8000000 INFO @ Tue, 16 Jun 2020 09:29:50: 3000000 INFO @ Tue, 16 Jun 2020 09:29:54: 9000000 INFO @ Tue, 16 Jun 2020 09:29:56: 4000000 INFO @ Tue, 16 Jun 2020 09:29:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:57: #1 total tags in treatment: 9425923 INFO @ Tue, 16 Jun 2020 09:29:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:57: #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 09:29:57: #1 tags after filtering in treatment: 9425923 INFO @ Tue, 16 Jun 2020 09:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:58: #2 number of paired peaks: 794 WARNING @ Tue, 16 Jun 2020 09:29:58: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:58: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:29:58: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:58: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:29:58: #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 09:29:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:58: #3 Pre-compute pvalue-qvalue table... 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 09:30:01: 5000000 INFO @ Tue, 16 Jun 2020 09:30:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.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 09:30:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:07: 6000000 INFO @ Tue, 16 Jun 2020 09:30:09: 1000000 INFO @ Tue, 16 Jun 2020 09:30:13: 7000000 INFO @ Tue, 16 Jun 2020 09:30:14: 2000000 INFO @ Tue, 16 Jun 2020 09:30:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:19: 8000000 INFO @ Tue, 16 Jun 2020 09:30:20: 3000000 INFO @ Tue, 16 Jun 2020 09:30:25: 9000000 INFO @ Tue, 16 Jun 2020 09:30:26: 4000000 INFO @ Tue, 16 Jun 2020 09:30:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:28: #1 total tags in treatment: 9425923 INFO @ Tue, 16 Jun 2020 09:30:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:28: #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 09:30:28: #1 tags after filtering in treatment: 9425923 INFO @ Tue, 16 Jun 2020 09:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:28: #2 number of paired peaks: 794 WARNING @ Tue, 16 Jun 2020 09:30:28: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:29: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:30:29: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.10_model.r WARNING @ Tue, 16 Jun 2020 09:30:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:29: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:30:29: #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 09:30:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.05_summits.bed INFO @ Tue, 16 Jun 2020 09:30:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2016 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:32: 5000000 INFO @ Tue, 16 Jun 2020 09:30:37: 6000000 INFO @ Tue, 16 Jun 2020 09:30:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:48: 8000000 INFO @ Tue, 16 Jun 2020 09:30:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:54: 9000000 INFO @ Tue, 16 Jun 2020 09:30:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:56: #1 total tags in treatment: 9425923 INFO @ Tue, 16 Jun 2020 09:30:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:56: #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 09:30:56: #1 tags after filtering in treatment: 9425923 INFO @ Tue, 16 Jun 2020 09:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:57: #2 number of paired peaks: 794 WARNING @ Tue, 16 Jun 2020 09:30:57: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:57: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:30:57: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:57: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:30:57: #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 09:30:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (843 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:31:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495040/SRX495040.20_summits.bed INFO @ Tue, 16 Jun 2020 09:31:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (271 records, 4 fields): 1 millis CompletedMACS2peakCalling