Job ID = 6366723 SRX = SRX2228876 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:58:38 prefetch.2.10.7: 1) Downloading 'SRR4380332'... 2020-06-15T22:58:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:36 prefetch.2.10.7: 'SRR4380332' is valid 2020-06-15T22:59:36 prefetch.2.10.7: 1) 'SRR4380332' was downloaded successfully Read 14851943 spots for SRR4380332/SRR4380332.sra Written 14851943 spots for SRR4380332/SRR4380332.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: 00:02:52 14851943 reads; of these: 14851943 (100.00%) were unpaired; of these: 5473288 (36.85%) aligned 0 times 7679733 (51.71%) aligned exactly 1 time 1698922 (11.44%) aligned >1 times 63.15% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 3805546 / 9378655 = 0.4058 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 08:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.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 08:05:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:04: 1000000 INFO @ Tue, 16 Jun 2020 08:06:10: 2000000 INFO @ Tue, 16 Jun 2020 08:06:16: 3000000 INFO @ Tue, 16 Jun 2020 08:06:23: 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 08:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.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 08:06:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:29: 5000000 INFO @ Tue, 16 Jun 2020 08:06:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:32: #1 total tags in treatment: 5573109 INFO @ Tue, 16 Jun 2020 08:06:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:32: #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 08:06:32: #1 tags after filtering in treatment: 5573109 INFO @ Tue, 16 Jun 2020 08:06:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:33: #2 number of paired peaks: 502 WARNING @ Tue, 16 Jun 2020 08:06:33: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:33: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:06:33: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 08:06:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:33: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 08:06:33: #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 08:06:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:34: 1000000 INFO @ Tue, 16 Jun 2020 08:06:39: 2000000 INFO @ Tue, 16 Jun 2020 08:06:45: 3000000 INFO @ Tue, 16 Jun 2020 08:06:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:50: 4000000 INFO @ Tue, 16 Jun 2020 08:06:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (643 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:55: 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 08:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.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 08:06:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:58: #1 total tags in treatment: 5573109 INFO @ Tue, 16 Jun 2020 08:06:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:58: #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 08:06:58: #1 tags after filtering in treatment: 5573109 INFO @ Tue, 16 Jun 2020 08:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:59: #2 number of paired peaks: 502 WARNING @ Tue, 16 Jun 2020 08:06:59: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:59: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:06:59: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 08:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:59: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 08:06:59: #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 08:06:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:03: 1000000 INFO @ Tue, 16 Jun 2020 08:07:09: 2000000 INFO @ Tue, 16 Jun 2020 08:07:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:14: 3000000 INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:20: 4000000 INFO @ Tue, 16 Jun 2020 08:07:25: 5000000 INFO @ Tue, 16 Jun 2020 08:07:29: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:29: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:29: #1 total tags in treatment: 5573109 INFO @ Tue, 16 Jun 2020 08:07:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:29: #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 08:07:29: #1 tags after filtering in treatment: 5573109 INFO @ Tue, 16 Jun 2020 08:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:29: #2 number of paired peaks: 502 WARNING @ Tue, 16 Jun 2020 08:07:29: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:07:29: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 08:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:29: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 08:07:29: #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 08:07:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228876/SRX2228876.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling