Job ID = 6366724 SRX = SRX2228877 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:23 prefetch.2.10.7: 1) Downloading 'SRR4380333'... 2020-06-15T22:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:19 prefetch.2.10.7: 'SRR4380333' is valid 2020-06-15T23:00:19 prefetch.2.10.7: 1) 'SRR4380333' was downloaded successfully Read 9681803 spots for SRR4380333/SRR4380333.sra Written 9681803 spots for SRR4380333/SRR4380333.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: 00:02:05 9681803 reads; of these: 9681803 (100.00%) were unpaired; of these: 2331890 (24.09%) aligned 0 times 5833460 (60.25%) aligned exactly 1 time 1516453 (15.66%) aligned >1 times 75.91% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 937725 / 7349913 = 0.1276 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 08:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.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 08:05:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:26: 1000000 INFO @ Tue, 16 Jun 2020 08:05:32: 2000000 INFO @ Tue, 16 Jun 2020 08:05:37: 3000000 INFO @ Tue, 16 Jun 2020 08:05:43: 4000000 INFO @ Tue, 16 Jun 2020 08:05:48: 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 08:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.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 08:05:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:54: 6000000 INFO @ Tue, 16 Jun 2020 08:05:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:05:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:05:57: #1 total tags in treatment: 6412188 INFO @ Tue, 16 Jun 2020 08:05:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:57: #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 08:05:57: #1 tags after filtering in treatment: 6412188 INFO @ Tue, 16 Jun 2020 08:05:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:57: 1000000 INFO @ Tue, 16 Jun 2020 08:05:57: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:05:57: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:57: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:05:57: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.05_model.r WARNING @ Tue, 16 Jun 2020 08:05:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:57: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:05:57: #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 08:05:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:02: 2000000 INFO @ Tue, 16 Jun 2020 08:06:08: 3000000 INFO @ Tue, 16 Jun 2020 08:06:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:13: 4000000 INFO @ Tue, 16 Jun 2020 08:06:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (703 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:19: 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 08:06:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.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 08:06:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:25: 6000000 INFO @ Tue, 16 Jun 2020 08:06:27: 1000000 INFO @ Tue, 16 Jun 2020 08:06:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:27: #1 total tags in treatment: 6412188 INFO @ Tue, 16 Jun 2020 08:06:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:27: #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 08:06:27: #1 tags after filtering in treatment: 6412188 INFO @ Tue, 16 Jun 2020 08:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:28: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:06:28: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:28: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:06:28: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:28: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:06:28: #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 08:06:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:32: 2000000 INFO @ Tue, 16 Jun 2020 08:06:38: 3000000 INFO @ Tue, 16 Jun 2020 08:06:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:43: 4000000 INFO @ Tue, 16 Jun 2020 08:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:49: 5000000 INFO @ Tue, 16 Jun 2020 08:06:55: 6000000 INFO @ Tue, 16 Jun 2020 08:06:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:57: #1 total tags in treatment: 6412188 INFO @ Tue, 16 Jun 2020 08:06:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:57: #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 08:06:57: #1 tags after filtering in treatment: 6412188 INFO @ Tue, 16 Jun 2020 08:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:57: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:58: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:06:58: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:58: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:58: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:06:58: #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 08:06:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228877/SRX2228877.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling