Job ID = 6367631 SRX = SRX3583343 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:14 prefetch.2.10.7: 1) Downloading 'SRR6493999'... 2020-06-15T23:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:34 prefetch.2.10.7: 1) 'SRR6493999' was downloaded successfully 2020-06-15T23:43:34 prefetch.2.10.7: 'SRR6493999' has 0 unresolved dependencies Read 32500265 spots for SRR6493999/SRR6493999.sra Written 32500265 spots for SRR6493999/SRR6493999.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: 00:10:48 32500265 reads; of these: 32500265 (100.00%) were unpaired; of these: 826785 (2.54%) aligned 0 times 27372200 (84.22%) aligned exactly 1 time 4301280 (13.23%) aligned >1 times 97.46% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 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 16 files... [bam_rmdupse_core] 5331571 / 31673480 = 0.1683 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 09:04:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.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 09:04:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:03: 1000000 INFO @ Tue, 16 Jun 2020 09:05:09: 2000000 INFO @ Tue, 16 Jun 2020 09:05:16: 3000000 INFO @ Tue, 16 Jun 2020 09:05:23: 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 09:05:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.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 09:05:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:30: 5000000 INFO @ Tue, 16 Jun 2020 09:05:34: 1000000 INFO @ Tue, 16 Jun 2020 09:05:37: 6000000 INFO @ Tue, 16 Jun 2020 09:05:41: 2000000 INFO @ Tue, 16 Jun 2020 09:05:44: 7000000 INFO @ Tue, 16 Jun 2020 09:05:49: 3000000 INFO @ Tue, 16 Jun 2020 09:05:52: 8000000 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 09:05:56: 4000000 INFO @ Tue, 16 Jun 2020 09:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.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 09:05:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:59: 9000000 INFO @ Tue, 16 Jun 2020 09:06:04: 5000000 INFO @ Tue, 16 Jun 2020 09:06:05: 1000000 INFO @ Tue, 16 Jun 2020 09:06:08: 10000000 INFO @ Tue, 16 Jun 2020 09:06:13: 6000000 INFO @ Tue, 16 Jun 2020 09:06:14: 2000000 INFO @ Tue, 16 Jun 2020 09:06:16: 11000000 INFO @ Tue, 16 Jun 2020 09:06:21: 7000000 INFO @ Tue, 16 Jun 2020 09:06:23: 3000000 INFO @ Tue, 16 Jun 2020 09:06:25: 12000000 INFO @ Tue, 16 Jun 2020 09:06:30: 8000000 INFO @ Tue, 16 Jun 2020 09:06:32: 4000000 INFO @ Tue, 16 Jun 2020 09:06:33: 13000000 INFO @ Tue, 16 Jun 2020 09:06:38: 9000000 INFO @ Tue, 16 Jun 2020 09:06:41: 14000000 INFO @ Tue, 16 Jun 2020 09:06:42: 5000000 INFO @ Tue, 16 Jun 2020 09:06:46: 10000000 INFO @ Tue, 16 Jun 2020 09:06:50: 15000000 INFO @ Tue, 16 Jun 2020 09:06:51: 6000000 INFO @ Tue, 16 Jun 2020 09:06:55: 11000000 INFO @ Tue, 16 Jun 2020 09:06:58: 16000000 INFO @ Tue, 16 Jun 2020 09:07:00: 7000000 INFO @ Tue, 16 Jun 2020 09:07:03: 12000000 INFO @ Tue, 16 Jun 2020 09:07:06: 17000000 INFO @ Tue, 16 Jun 2020 09:07:09: 8000000 INFO @ Tue, 16 Jun 2020 09:07:11: 13000000 INFO @ Tue, 16 Jun 2020 09:07:15: 18000000 INFO @ Tue, 16 Jun 2020 09:07:19: 9000000 INFO @ Tue, 16 Jun 2020 09:07:20: 14000000 INFO @ Tue, 16 Jun 2020 09:07:23: 19000000 INFO @ Tue, 16 Jun 2020 09:07:28: 10000000 INFO @ Tue, 16 Jun 2020 09:07:28: 15000000 INFO @ Tue, 16 Jun 2020 09:07:31: 20000000 INFO @ Tue, 16 Jun 2020 09:07:36: 16000000 INFO @ Tue, 16 Jun 2020 09:07:37: 11000000 INFO @ Tue, 16 Jun 2020 09:07:40: 21000000 INFO @ Tue, 16 Jun 2020 09:07:44: 17000000 INFO @ Tue, 16 Jun 2020 09:07:46: 12000000 INFO @ Tue, 16 Jun 2020 09:07:48: 22000000 INFO @ Tue, 16 Jun 2020 09:07:53: 18000000 INFO @ Tue, 16 Jun 2020 09:07:55: 13000000 INFO @ Tue, 16 Jun 2020 09:07:56: 23000000 INFO @ Tue, 16 Jun 2020 09:08:01: 19000000 INFO @ Tue, 16 Jun 2020 09:08:04: 14000000 INFO @ Tue, 16 Jun 2020 09:08:04: 24000000 INFO @ Tue, 16 Jun 2020 09:08:09: 20000000 INFO @ Tue, 16 Jun 2020 09:08:12: 25000000 INFO @ Tue, 16 Jun 2020 09:08:13: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:17: 21000000 INFO @ Tue, 16 Jun 2020 09:08:20: 26000000 INFO @ Tue, 16 Jun 2020 09:08:22: 16000000 INFO @ Tue, 16 Jun 2020 09:08:23: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:08:23: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:08:23: #1 total tags in treatment: 26341909 INFO @ Tue, 16 Jun 2020 09:08:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:23: #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 09:08:24: #1 tags after filtering in treatment: 26341909 INFO @ Tue, 16 Jun 2020 09:08:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:25: 22000000 INFO @ Tue, 16 Jun 2020 09:08:25: #2 number of paired peaks: 147 WARNING @ Tue, 16 Jun 2020 09:08:25: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:26: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:08:26: #2 alternative fragment length(s) may be 2,78 bps INFO @ Tue, 16 Jun 2020 09:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.05_model.r WARNING @ Tue, 16 Jun 2020 09:08:26: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:26: #2 You may need to consider one of the other alternative d(s): 2,78 WARNING @ Tue, 16 Jun 2020 09:08:26: #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 09:08:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:31: 17000000 INFO @ Tue, 16 Jun 2020 09:08:33: 23000000 INFO @ Tue, 16 Jun 2020 09:08:39: 18000000 INFO @ Tue, 16 Jun 2020 09:08:41: 24000000 INFO @ Tue, 16 Jun 2020 09:08:48: 19000000 INFO @ Tue, 16 Jun 2020 09:08:49: 25000000 INFO @ Tue, 16 Jun 2020 09:08:57: 26000000 INFO @ Tue, 16 Jun 2020 09:08:58: 20000000 INFO @ Tue, 16 Jun 2020 09:09:00: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:09:00: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:09:00: #1 total tags in treatment: 26341909 INFO @ Tue, 16 Jun 2020 09:09:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:00: #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 09:09:00: #1 tags after filtering in treatment: 26341909 INFO @ Tue, 16 Jun 2020 09:09:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:02: #2 number of paired peaks: 147 WARNING @ Tue, 16 Jun 2020 09:09:02: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:02: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:09:02: #2 alternative fragment length(s) may be 2,78 bps INFO @ Tue, 16 Jun 2020 09:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.10_model.r WARNING @ Tue, 16 Jun 2020 09:09:02: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:02: #2 You may need to consider one of the other alternative d(s): 2,78 WARNING @ Tue, 16 Jun 2020 09:09:02: #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 09:09:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:06: 21000000 INFO @ Tue, 16 Jun 2020 09:09:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:09:14: 22000000 INFO @ Tue, 16 Jun 2020 09:09:22: 23000000 INFO @ Tue, 16 Jun 2020 09:09:30: 24000000 INFO @ Tue, 16 Jun 2020 09:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4172 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:38: 25000000 INFO @ Tue, 16 Jun 2020 09:09:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:46: 26000000 INFO @ Tue, 16 Jun 2020 09:09:48: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:09:48: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:09:48: #1 total tags in treatment: 26341909 INFO @ Tue, 16 Jun 2020 09:09:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:48: #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 09:09:49: #1 tags after filtering in treatment: 26341909 INFO @ Tue, 16 Jun 2020 09:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:51: #2 number of paired peaks: 147 WARNING @ Tue, 16 Jun 2020 09:09:51: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:51: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:09:51: #2 alternative fragment length(s) may be 2,78 bps INFO @ Tue, 16 Jun 2020 09:09:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:51: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:51: #2 You may need to consider one of the other alternative d(s): 2,78 WARNING @ Tue, 16 Jun 2020 09:09:51: #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 09:09:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3053 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583343/SRX3583343.20_summits.bed INFO @ Tue, 16 Jun 2020 09:10:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1694 records, 4 fields): 3 millis CompletedMACS2peakCalling