Job ID = 6368579 SRX = SRX5020805 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:31 prefetch.2.10.7: 1) Downloading 'SRR8201428'... 2020-06-16T00:25:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:42 prefetch.2.10.7: 1) 'SRR8201428' was downloaded successfully 2020-06-16T00:27:42 prefetch.2.10.7: 'SRR8201428' has 0 unresolved dependencies Read 22530091 spots for SRR8201428/SRR8201428.sra Written 22530091 spots for SRR8201428/SRR8201428.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: 00:07:01 22530091 reads; of these: 22530091 (100.00%) were unpaired; of these: 875660 (3.89%) aligned 0 times 18108808 (80.38%) aligned exactly 1 time 3545623 (15.74%) aligned >1 times 96.11% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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 12 files... [bam_rmdupse_core] 3067926 / 21654431 = 0.1417 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 09:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.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 09:41:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:37: 1000000 INFO @ Tue, 16 Jun 2020 09:41:43: 2000000 INFO @ Tue, 16 Jun 2020 09:41:49: 3000000 INFO @ Tue, 16 Jun 2020 09:41:55: 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 09:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.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 09:42:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:01: 5000000 INFO @ Tue, 16 Jun 2020 09:42:08: 1000000 INFO @ Tue, 16 Jun 2020 09:42:08: 6000000 INFO @ Tue, 16 Jun 2020 09:42:14: 2000000 INFO @ Tue, 16 Jun 2020 09:42:15: 7000000 INFO @ Tue, 16 Jun 2020 09:42:21: 3000000 INFO @ Tue, 16 Jun 2020 09:42:22: 8000000 INFO @ Tue, 16 Jun 2020 09:42:28: 4000000 INFO @ Tue, 16 Jun 2020 09:42:29: 9000000 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 09:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.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 09:42:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:35: 5000000 INFO @ Tue, 16 Jun 2020 09:42:36: 10000000 INFO @ Tue, 16 Jun 2020 09:42:38: 1000000 INFO @ Tue, 16 Jun 2020 09:42:43: 6000000 INFO @ Tue, 16 Jun 2020 09:42:44: 11000000 INFO @ Tue, 16 Jun 2020 09:42:46: 2000000 INFO @ Tue, 16 Jun 2020 09:42:51: 7000000 INFO @ Tue, 16 Jun 2020 09:42:51: 12000000 INFO @ Tue, 16 Jun 2020 09:42:53: 3000000 INFO @ Tue, 16 Jun 2020 09:42:59: 8000000 INFO @ Tue, 16 Jun 2020 09:42:59: 13000000 INFO @ Tue, 16 Jun 2020 09:43:00: 4000000 INFO @ Tue, 16 Jun 2020 09:43:06: 9000000 INFO @ Tue, 16 Jun 2020 09:43:06: 14000000 INFO @ Tue, 16 Jun 2020 09:43:08: 5000000 INFO @ Tue, 16 Jun 2020 09:43:13: 15000000 INFO @ Tue, 16 Jun 2020 09:43:13: 10000000 INFO @ Tue, 16 Jun 2020 09:43:15: 6000000 INFO @ Tue, 16 Jun 2020 09:43:21: 16000000 INFO @ Tue, 16 Jun 2020 09:43:21: 11000000 INFO @ Tue, 16 Jun 2020 09:43:22: 7000000 INFO @ Tue, 16 Jun 2020 09:43:28: 17000000 INFO @ Tue, 16 Jun 2020 09:43:28: 12000000 INFO @ Tue, 16 Jun 2020 09:43:29: 8000000 INFO @ Tue, 16 Jun 2020 09:43:35: 18000000 INFO @ Tue, 16 Jun 2020 09:43:35: 13000000 INFO @ Tue, 16 Jun 2020 09:43:36: 9000000 INFO @ Tue, 16 Jun 2020 09:43:39: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:43:39: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:43:39: #1 total tags in treatment: 18586505 INFO @ Tue, 16 Jun 2020 09:43:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:43:39: #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 09:43:40: #1 tags after filtering in treatment: 18586505 INFO @ Tue, 16 Jun 2020 09:43:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:43:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:43:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:43:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:43:41: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:43:41: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:43:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:43:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:43:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:43:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:43:41: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 09:43:41: #2 alternative fragment length(s) may be 2,64,562 bps INFO @ Tue, 16 Jun 2020 09:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.05_model.r WARNING @ Tue, 16 Jun 2020 09:43:41: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:43:41: #2 You may need to consider one of the other alternative d(s): 2,64,562 WARNING @ Tue, 16 Jun 2020 09:43:41: #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 09:43:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:43:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:43:43: 14000000 INFO @ Tue, 16 Jun 2020 09:43:43: 10000000 INFO @ Tue, 16 Jun 2020 09:43:50: 15000000 INFO @ Tue, 16 Jun 2020 09:43:50: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:57: 16000000 INFO @ Tue, 16 Jun 2020 09:43:57: 12000000 INFO @ Tue, 16 Jun 2020 09:44:04: 17000000 INFO @ Tue, 16 Jun 2020 09:44:04: 13000000 INFO @ Tue, 16 Jun 2020 09:44:11: 18000000 INFO @ Tue, 16 Jun 2020 09:44:11: 14000000 INFO @ Tue, 16 Jun 2020 09:44:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:15: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:44:15: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:44:15: #1 total tags in treatment: 18586505 INFO @ Tue, 16 Jun 2020 09:44:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:15: #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 09:44:15: #1 tags after filtering in treatment: 18586505 INFO @ Tue, 16 Jun 2020 09:44:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:16: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:44:16: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:16: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 09:44:16: #2 alternative fragment length(s) may be 2,64,562 bps INFO @ Tue, 16 Jun 2020 09:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.10_model.r WARNING @ Tue, 16 Jun 2020 09:44:16: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:16: #2 You may need to consider one of the other alternative d(s): 2,64,562 WARNING @ Tue, 16 Jun 2020 09:44:16: #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 09:44:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:18: 15000000 INFO @ Tue, 16 Jun 2020 09:44:25: 16000000 INFO @ Tue, 16 Jun 2020 09:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (710 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:31: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:37: 18000000 INFO @ Tue, 16 Jun 2020 09:44:41: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:44:41: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:44:41: #1 total tags in treatment: 18586505 INFO @ Tue, 16 Jun 2020 09:44:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:41: #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 09:44:41: #1 tags after filtering in treatment: 18586505 INFO @ Tue, 16 Jun 2020 09:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:42: #2 number of paired peaks: 209 WARNING @ Tue, 16 Jun 2020 09:44:42: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:43: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 09:44:43: #2 alternative fragment length(s) may be 2,64,562 bps INFO @ Tue, 16 Jun 2020 09:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:43: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:43: #2 You may need to consider one of the other alternative d(s): 2,64,562 WARNING @ Tue, 16 Jun 2020 09:44:43: #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 09:44:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.10_summits.bed INFO @ Tue, 16 Jun 2020 09:45:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (478 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020805/SRX5020805.20_summits.bed INFO @ Tue, 16 Jun 2020 09:45:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (250 records, 4 fields): 1 millis CompletedMACS2peakCalling