Job ID = 6368749 SRX = SRX5402772 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:38:49 prefetch.2.10.7: 1) Downloading 'SRR8603006'... 2020-06-16T00:38:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:00 prefetch.2.10.7: 1) 'SRR8603006' was downloaded successfully Read 19673243 spots for SRR8603006/SRR8603006.sra Written 19673243 spots for SRR8603006/SRR8603006.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: 00:04:03 19673243 reads; of these: 19673243 (100.00%) were unpaired; of these: 3956385 (20.11%) aligned 0 times 12933257 (65.74%) aligned exactly 1 time 2783601 (14.15%) aligned >1 times 79.89% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 1438058 / 15716858 = 0.0915 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 09:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.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 09:51:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:31: 1000000 INFO @ Tue, 16 Jun 2020 09:51:36: 2000000 INFO @ Tue, 16 Jun 2020 09:51:41: 3000000 INFO @ Tue, 16 Jun 2020 09:51:46: 4000000 INFO @ Tue, 16 Jun 2020 09:51:51: 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 09:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.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 09:51:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:56: 6000000 INFO @ Tue, 16 Jun 2020 09:52:00: 1000000 INFO @ Tue, 16 Jun 2020 09:52:01: 7000000 INFO @ Tue, 16 Jun 2020 09:52:06: 2000000 INFO @ Tue, 16 Jun 2020 09:52:07: 8000000 INFO @ Tue, 16 Jun 2020 09:52:11: 3000000 INFO @ Tue, 16 Jun 2020 09:52:12: 9000000 INFO @ Tue, 16 Jun 2020 09:52:16: 4000000 INFO @ Tue, 16 Jun 2020 09:52:17: 10000000 INFO @ Tue, 16 Jun 2020 09:52:21: 5000000 INFO @ Tue, 16 Jun 2020 09:52:22: 11000000 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 09:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.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 09:52:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:26: 6000000 INFO @ Tue, 16 Jun 2020 09:52:28: 12000000 INFO @ Tue, 16 Jun 2020 09:52:31: 1000000 INFO @ Tue, 16 Jun 2020 09:52:32: 7000000 INFO @ Tue, 16 Jun 2020 09:52:33: 13000000 INFO @ Tue, 16 Jun 2020 09:52:36: 2000000 INFO @ Tue, 16 Jun 2020 09:52:37: 8000000 INFO @ Tue, 16 Jun 2020 09:52:38: 14000000 INFO @ Tue, 16 Jun 2020 09:52:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:40: #1 total tags in treatment: 14278800 INFO @ Tue, 16 Jun 2020 09:52:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:40: #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 09:52:40: #1 tags after filtering in treatment: 14278800 INFO @ Tue, 16 Jun 2020 09:52:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:41: #2 number of paired peaks: 301 WARNING @ Tue, 16 Jun 2020 09:52:41: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:41: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:52:41: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:41: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:41: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:52:41: #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 09:52:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:41: 3000000 INFO @ Tue, 16 Jun 2020 09:52:42: 9000000 INFO @ Tue, 16 Jun 2020 09:52:47: 4000000 INFO @ Tue, 16 Jun 2020 09:52:48: 10000000 INFO @ Tue, 16 Jun 2020 09:52:52: 5000000 INFO @ Tue, 16 Jun 2020 09:52:53: 11000000 INFO @ Tue, 16 Jun 2020 09:52:57: 6000000 INFO @ Tue, 16 Jun 2020 09:52:58: 12000000 INFO @ Tue, 16 Jun 2020 09:53:02: 7000000 INFO @ Tue, 16 Jun 2020 09:53:03: 13000000 INFO @ Tue, 16 Jun 2020 09:53:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:07: 8000000 INFO @ Tue, 16 Jun 2020 09:53:08: 14000000 INFO @ Tue, 16 Jun 2020 09:53:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:10: #1 total tags in treatment: 14278800 INFO @ Tue, 16 Jun 2020 09:53:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:10: #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 09:53:10: #1 tags after filtering in treatment: 14278800 INFO @ Tue, 16 Jun 2020 09:53:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:11: #2 number of paired peaks: 301 WARNING @ Tue, 16 Jun 2020 09:53:11: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:11: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:53:11: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.10_model.r WARNING @ Tue, 16 Jun 2020 09:53:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:11: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:53:11: #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 09:53:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:13: 9000000 INFO @ Tue, 16 Jun 2020 09:53:18: 10000000 INFO @ Tue, 16 Jun 2020 09:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:23: 11000000 INFO @ Tue, 16 Jun 2020 09:53:28: 12000000 INFO @ Tue, 16 Jun 2020 09:53:33: 13000000 INFO @ Tue, 16 Jun 2020 09:53:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:38: 14000000 INFO @ Tue, 16 Jun 2020 09:53:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:39: #1 total tags in treatment: 14278800 INFO @ Tue, 16 Jun 2020 09:53:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:39: #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 09:53:39: #1 tags after filtering in treatment: 14278800 INFO @ Tue, 16 Jun 2020 09:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:40: #2 number of paired peaks: 301 WARNING @ Tue, 16 Jun 2020 09:53:40: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:40: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:53:40: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.20_model.r WARNING @ Tue, 16 Jun 2020 09:53:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:40: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:53:40: #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 09:53:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (453 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402772/SRX5402772.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling