Job ID = 6368347 SRX = SRX495028 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:05 prefetch.2.10.7: 1) Downloading 'SRR1198560'... 2020-06-16T00:13:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:18 prefetch.2.10.7: 1) 'SRR1198560' was downloaded successfully Read 22906742 spots for SRR1198560/SRR1198560.sra Written 22906742 spots for SRR1198560/SRR1198560.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: 00:04:51 22906742 reads; of these: 22906742 (100.00%) were unpaired; of these: 3075581 (13.43%) aligned 0 times 16016498 (69.92%) aligned exactly 1 time 3814663 (16.65%) aligned >1 times 86.57% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 2900048 / 19831161 = 0.1462 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 09:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.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 09:27:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:13: 1000000 INFO @ Tue, 16 Jun 2020 09:27:19: 2000000 INFO @ Tue, 16 Jun 2020 09:27:24: 3000000 INFO @ Tue, 16 Jun 2020 09:27:30: 4000000 INFO @ Tue, 16 Jun 2020 09:27:35: 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 09:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.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 09:27:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:41: 6000000 INFO @ Tue, 16 Jun 2020 09:27:43: 1000000 INFO @ Tue, 16 Jun 2020 09:27:46: 7000000 INFO @ Tue, 16 Jun 2020 09:27:49: 2000000 INFO @ Tue, 16 Jun 2020 09:27:52: 8000000 INFO @ Tue, 16 Jun 2020 09:27:54: 3000000 INFO @ Tue, 16 Jun 2020 09:27:58: 9000000 INFO @ Tue, 16 Jun 2020 09:28:00: 4000000 INFO @ Tue, 16 Jun 2020 09:28:04: 10000000 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 09:28:06: 5000000 INFO @ Tue, 16 Jun 2020 09:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.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 09:28:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:10: 11000000 INFO @ Tue, 16 Jun 2020 09:28:12: 6000000 INFO @ Tue, 16 Jun 2020 09:28:14: 1000000 INFO @ Tue, 16 Jun 2020 09:28:16: 12000000 INFO @ Tue, 16 Jun 2020 09:28:18: 7000000 INFO @ Tue, 16 Jun 2020 09:28:20: 2000000 INFO @ Tue, 16 Jun 2020 09:28:22: 13000000 INFO @ Tue, 16 Jun 2020 09:28:25: 8000000 INFO @ Tue, 16 Jun 2020 09:28:26: 3000000 INFO @ Tue, 16 Jun 2020 09:28:29: 14000000 INFO @ Tue, 16 Jun 2020 09:28:31: 9000000 INFO @ Tue, 16 Jun 2020 09:28:32: 4000000 INFO @ Tue, 16 Jun 2020 09:28:35: 15000000 INFO @ Tue, 16 Jun 2020 09:28:37: 10000000 INFO @ Tue, 16 Jun 2020 09:28:39: 5000000 INFO @ Tue, 16 Jun 2020 09:28:41: 16000000 INFO @ Tue, 16 Jun 2020 09:28:44: 11000000 INFO @ Tue, 16 Jun 2020 09:28:45: 6000000 INFO @ Tue, 16 Jun 2020 09:28:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:47: #1 total tags in treatment: 16931113 INFO @ Tue, 16 Jun 2020 09:28:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:47: #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 09:28:47: #1 tags after filtering in treatment: 16931113 INFO @ Tue, 16 Jun 2020 09:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:49: #2 number of paired peaks: 218 WARNING @ Tue, 16 Jun 2020 09:28:49: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:49: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:28:49: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.05_model.r WARNING @ Tue, 16 Jun 2020 09:28:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:49: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:28:49: #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 09:28:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:50: 12000000 INFO @ Tue, 16 Jun 2020 09:28:52: 7000000 INFO @ Tue, 16 Jun 2020 09:28:56: 13000000 INFO @ Tue, 16 Jun 2020 09:28:58: 8000000 INFO @ Tue, 16 Jun 2020 09:29:03: 14000000 INFO @ Tue, 16 Jun 2020 09:29:04: 9000000 INFO @ Tue, 16 Jun 2020 09:29:09: 15000000 INFO @ Tue, 16 Jun 2020 09:29:11: 10000000 INFO @ Tue, 16 Jun 2020 09:29:15: 16000000 INFO @ Tue, 16 Jun 2020 09:29:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:17: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:21: #1 total tags in treatment: 16931113 INFO @ Tue, 16 Jun 2020 09:29:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:21: #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 09:29:22: #1 tags after filtering in treatment: 16931113 INFO @ Tue, 16 Jun 2020 09:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:23: #2 number of paired peaks: 218 WARNING @ Tue, 16 Jun 2020 09:29:23: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:23: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:29:23: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:23: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:29:23: #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 09:29:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:24: 12000000 INFO @ Tue, 16 Jun 2020 09:29:30: 13000000 INFO @ Tue, 16 Jun 2020 09:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2584 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:35: 14000000 INFO @ Tue, 16 Jun 2020 09:29:41: 15000000 INFO @ Tue, 16 Jun 2020 09:29:47: 16000000 INFO @ Tue, 16 Jun 2020 09:29:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:52: #1 total tags in treatment: 16931113 INFO @ Tue, 16 Jun 2020 09:29:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:52: #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 09:29:52: #1 tags after filtering in treatment: 16931113 INFO @ Tue, 16 Jun 2020 09:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:53: #2 number of paired peaks: 218 WARNING @ Tue, 16 Jun 2020 09:29:53: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:54: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:29:54: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:29:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.20_model.r WARNING @ Tue, 16 Jun 2020 09:29:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:54: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:29:54: #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 09:29:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (708 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495028/SRX495028.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling