Job ID = 6507868 SRX = SRX494949 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:19:48 prefetch.2.10.7: 1) Downloading 'SRR1198481'... 2020-06-26T13:19:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:21:14 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:21:15 prefetch.2.10.7: 'SRR1198481' is valid 2020-06-26T13:21:15 prefetch.2.10.7: 1) 'SRR1198481' was downloaded successfully Read 20769458 spots for SRR1198481/SRR1198481.sra Written 20769458 spots for SRR1198481/SRR1198481.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: 00:03:28 20769458 reads; of these: 20769458 (100.00%) were unpaired; of these: 275870 (1.33%) aligned 0 times 16889624 (81.32%) aligned exactly 1 time 3603964 (17.35%) aligned >1 times 98.67% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 2970715 / 20493588 = 0.1450 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 @ Fri, 26 Jun 2020 22:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.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 @ Fri, 26 Jun 2020 22:29:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:29:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:44: 1000000 INFO @ Fri, 26 Jun 2020 22:29:48: 2000000 INFO @ Fri, 26 Jun 2020 22:29:53: 3000000 INFO @ Fri, 26 Jun 2020 22:29:58: 4000000 INFO @ Fri, 26 Jun 2020 22:30:03: 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 @ Fri, 26 Jun 2020 22:30:08: 6000000 INFO @ Fri, 26 Jun 2020 22:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.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 @ Fri, 26 Jun 2020 22:30:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:13: 7000000 INFO @ Fri, 26 Jun 2020 22:30:15: 1000000 INFO @ Fri, 26 Jun 2020 22:30:19: 8000000 INFO @ Fri, 26 Jun 2020 22:30:22: 2000000 INFO @ Fri, 26 Jun 2020 22:30:24: 9000000 INFO @ Fri, 26 Jun 2020 22:30:28: 3000000 INFO @ Fri, 26 Jun 2020 22:30:30: 10000000 INFO @ Fri, 26 Jun 2020 22:30:34: 4000000 INFO @ Fri, 26 Jun 2020 22:30:36: 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 @ Fri, 26 Jun 2020 22:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.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 @ Fri, 26 Jun 2020 22:30:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:40: 5000000 INFO @ Fri, 26 Jun 2020 22:30:41: 12000000 INFO @ Fri, 26 Jun 2020 22:30:45: 1000000 INFO @ Fri, 26 Jun 2020 22:30:47: 6000000 INFO @ Fri, 26 Jun 2020 22:30:47: 13000000 INFO @ Fri, 26 Jun 2020 22:30:52: 2000000 INFO @ Fri, 26 Jun 2020 22:30:53: 14000000 INFO @ Fri, 26 Jun 2020 22:30:53: 7000000 INFO @ Fri, 26 Jun 2020 22:30:58: 15000000 INFO @ Fri, 26 Jun 2020 22:30:58: 3000000 INFO @ Fri, 26 Jun 2020 22:30:59: 8000000 INFO @ Fri, 26 Jun 2020 22:31:04: 16000000 INFO @ Fri, 26 Jun 2020 22:31:05: 4000000 INFO @ Fri, 26 Jun 2020 22:31:05: 9000000 INFO @ Fri, 26 Jun 2020 22:31:10: 17000000 INFO @ Fri, 26 Jun 2020 22:31:11: 5000000 INFO @ Fri, 26 Jun 2020 22:31:11: 10000000 INFO @ Fri, 26 Jun 2020 22:31:13: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:31:13: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:31:13: #1 total tags in treatment: 17522873 INFO @ Fri, 26 Jun 2020 22:31:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:31:13: #1 tags after filtering in treatment: 17522873 INFO @ Fri, 26 Jun 2020 22:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:13: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:14: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 22:31:14: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:14: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:14: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:14: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:14: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:14: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 22:31:14: #2 alternative fragment length(s) may be 2,38,72 bps INFO @ Fri, 26 Jun 2020 22:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.05_model.r WARNING @ Fri, 26 Jun 2020 22:31:14: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:31:14: #2 You may need to consider one of the other alternative d(s): 2,38,72 WARNING @ Fri, 26 Jun 2020 22:31:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:31:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:31:17: 6000000 INFO @ Fri, 26 Jun 2020 22:31:18: 11000000 INFO @ Fri, 26 Jun 2020 22:31:23: 7000000 INFO @ Fri, 26 Jun 2020 22:31:24: 12000000 INFO @ Fri, 26 Jun 2020 22:31:29: 8000000 INFO @ Fri, 26 Jun 2020 22:31:30: 13000000 INFO @ Fri, 26 Jun 2020 22:31:35: 9000000 INFO @ Fri, 26 Jun 2020 22:31:36: 14000000 INFO @ Fri, 26 Jun 2020 22:31:41: 10000000 INFO @ Fri, 26 Jun 2020 22:31:42: 15000000 INFO @ Fri, 26 Jun 2020 22:31:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:31:48: 11000000 INFO @ Fri, 26 Jun 2020 22:31:49: 16000000 INFO @ Fri, 26 Jun 2020 22:31:54: 12000000 INFO @ Fri, 26 Jun 2020 22:31:55: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:31:58: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:31:58: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:31:58: #1 total tags in treatment: 17522873 INFO @ Fri, 26 Jun 2020 22:31:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:31:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:31:58: #1 tags after filtering in treatment: 17522873 INFO @ Fri, 26 Jun 2020 22:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:31:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:31:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:31:59: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 22:31:59: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 22:31:59: start model_add_line... INFO @ Fri, 26 Jun 2020 22:31:59: start X-correlation... INFO @ Fri, 26 Jun 2020 22:31:59: end of X-cor INFO @ Fri, 26 Jun 2020 22:31:59: #2 finished! INFO @ Fri, 26 Jun 2020 22:31:59: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 22:31:59: #2 alternative fragment length(s) may be 2,38,72 bps INFO @ Fri, 26 Jun 2020 22:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.10_model.r WARNING @ Fri, 26 Jun 2020 22:31:59: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:31:59: #2 You may need to consider one of the other alternative d(s): 2,38,72 WARNING @ Fri, 26 Jun 2020 22:31:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:31:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.05_summits.bed INFO @ Fri, 26 Jun 2020 22:32:00: 13000000 INFO @ Fri, 26 Jun 2020 22:32:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5315 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:32:06: 14000000 INFO @ Fri, 26 Jun 2020 22:32:12: 15000000 INFO @ Fri, 26 Jun 2020 22:32:18: 16000000 INFO @ Fri, 26 Jun 2020 22:32:23: 17000000 INFO @ Fri, 26 Jun 2020 22:32:26: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:32:26: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:32:26: #1 total tags in treatment: 17522873 INFO @ Fri, 26 Jun 2020 22:32:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:32:27: #1 tags after filtering in treatment: 17522873 INFO @ Fri, 26 Jun 2020 22:32:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:27: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:28: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 22:32:28: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:28: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 22:32:28: #2 alternative fragment length(s) may be 2,38,72 bps INFO @ Fri, 26 Jun 2020 22:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.20_model.r WARNING @ Fri, 26 Jun 2020 22:32:28: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:32:28: #2 You may need to consider one of the other alternative d(s): 2,38,72 WARNING @ Fri, 26 Jun 2020 22:32:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:32:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.10_summits.bed INFO @ Fri, 26 Jun 2020 22:32:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2502 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:32:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494949/SRX494949.20_summits.bed INFO @ Fri, 26 Jun 2020 22:33:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (552 records, 4 fields): 2 millis CompletedMACS2peakCalling