Job ID = 6368586 SRX = SRX5020812 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:03 prefetch.2.10.7: 1) Downloading 'SRR8201435'... 2020-06-16T00:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:45 prefetch.2.10.7: 'SRR8201435' is valid 2020-06-16T00:24:45 prefetch.2.10.7: 1) 'SRR8201435' was downloaded successfully Read 11135255 spots for SRR8201435/SRR8201435.sra Written 11135255 spots for SRR8201435/SRR8201435.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: 00:02:37 11135255 reads; of these: 11135255 (100.00%) were unpaired; of these: 101731 (0.91%) aligned 0 times 9167851 (82.33%) aligned exactly 1 time 1865673 (16.75%) aligned >1 times 99.09% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 798993 / 11033524 = 0.0724 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 09:31:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.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 09:31:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:24: 1000000 INFO @ Tue, 16 Jun 2020 09:31:30: 2000000 INFO @ Tue, 16 Jun 2020 09:31:36: 3000000 INFO @ Tue, 16 Jun 2020 09:31:42: 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 09:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.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 09:31:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:48: 5000000 INFO @ Tue, 16 Jun 2020 09:31:55: 6000000 INFO @ Tue, 16 Jun 2020 09:31:55: 1000000 INFO @ Tue, 16 Jun 2020 09:32:02: 7000000 INFO @ Tue, 16 Jun 2020 09:32:03: 2000000 INFO @ Tue, 16 Jun 2020 09:32:09: 8000000 INFO @ Tue, 16 Jun 2020 09:32:11: 3000000 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 09:32:17: 9000000 INFO @ Tue, 16 Jun 2020 09:32:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.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 09:32:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:19: 4000000 INFO @ Tue, 16 Jun 2020 09:32:24: 10000000 INFO @ Tue, 16 Jun 2020 09:32:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:25: #1 total tags in treatment: 10234531 INFO @ Tue, 16 Jun 2020 09:32:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:25: #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 09:32:25: 1000000 INFO @ Tue, 16 Jun 2020 09:32:25: #1 tags after filtering in treatment: 10234531 INFO @ Tue, 16 Jun 2020 09:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:26: #2 number of paired peaks: 314 WARNING @ Tue, 16 Jun 2020 09:32:26: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:26: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:32:26: #2 alternative fragment length(s) may be 3,49,596 bps INFO @ Tue, 16 Jun 2020 09:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.05_model.r WARNING @ Tue, 16 Jun 2020 09:32:26: #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 09:32:26: #2 You may need to consider one of the other alternative d(s): 3,49,596 WARNING @ Tue, 16 Jun 2020 09:32:26: #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 09:32:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:26: 5000000 INFO @ Tue, 16 Jun 2020 09:32:32: 2000000 INFO @ Tue, 16 Jun 2020 09:32:34: 6000000 INFO @ Tue, 16 Jun 2020 09:32:39: 3000000 INFO @ Tue, 16 Jun 2020 09:32:41: 7000000 INFO @ Tue, 16 Jun 2020 09:32:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:46: 4000000 INFO @ Tue, 16 Jun 2020 09:32:49: 8000000 INFO @ Tue, 16 Jun 2020 09:32:54: 5000000 INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (595 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:57: 9000000 INFO @ Tue, 16 Jun 2020 09:33:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:05: 10000000 INFO @ Tue, 16 Jun 2020 09:33:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:07: #1 total tags in treatment: 10234531 INFO @ Tue, 16 Jun 2020 09:33:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:07: #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 09:33:07: #1 tags after filtering in treatment: 10234531 INFO @ Tue, 16 Jun 2020 09:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:08: 7000000 INFO @ Tue, 16 Jun 2020 09:33:08: #2 number of paired peaks: 314 WARNING @ Tue, 16 Jun 2020 09:33:08: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:08: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:33:08: #2 alternative fragment length(s) may be 3,49,596 bps INFO @ Tue, 16 Jun 2020 09:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:08: #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 09:33:08: #2 You may need to consider one of the other alternative d(s): 3,49,596 WARNING @ Tue, 16 Jun 2020 09:33:08: #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 09:33:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:14: 8000000 INFO @ Tue, 16 Jun 2020 09:33:20: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:27: 10000000 INFO @ Tue, 16 Jun 2020 09:33:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:28: #1 total tags in treatment: 10234531 INFO @ Tue, 16 Jun 2020 09:33:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:28: #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 09:33:28: #1 tags after filtering in treatment: 10234531 INFO @ Tue, 16 Jun 2020 09:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:29: #2 number of paired peaks: 314 WARNING @ Tue, 16 Jun 2020 09:33:29: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:33:29: #2 alternative fragment length(s) may be 3,49,596 bps INFO @ Tue, 16 Jun 2020 09:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:29: #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 09:33:29: #2 You may need to consider one of the other alternative d(s): 3,49,596 WARNING @ Tue, 16 Jun 2020 09:33:29: #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 09:33:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020812/SRX5020812.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 1 millis CompletedMACS2peakCalling