Job ID = 6367278 SRX = SRX330988 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:01 prefetch.2.10.7: 1) Downloading 'SRR947193'... 2020-06-15T23:25:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:43 prefetch.2.10.7: 1) 'SRR947193' was downloaded successfully Read 12396180 spots for SRR947193/SRR947193.sra Written 12396180 spots for SRR947193/SRR947193.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: 00:04:48 12396180 reads; of these: 12396180 (100.00%) were unpaired; of these: 2127485 (17.16%) aligned 0 times 7753444 (62.55%) aligned exactly 1 time 2515251 (20.29%) aligned >1 times 82.84% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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 8 files... [bam_rmdupse_core] 1312629 / 10268695 = 0.1278 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 08:35:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.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 08:35:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:05: 1000000 INFO @ Tue, 16 Jun 2020 08:36:12: 2000000 INFO @ Tue, 16 Jun 2020 08:36:19: 3000000 INFO @ Tue, 16 Jun 2020 08:36:26: 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 08:36:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.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 08:36:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:33: 5000000 INFO @ Tue, 16 Jun 2020 08:36:35: 1000000 INFO @ Tue, 16 Jun 2020 08:36:41: 6000000 INFO @ Tue, 16 Jun 2020 08:36:42: 2000000 INFO @ Tue, 16 Jun 2020 08:36:48: 7000000 INFO @ Tue, 16 Jun 2020 08:36:48: 3000000 INFO @ Tue, 16 Jun 2020 08:36:55: 4000000 INFO @ Tue, 16 Jun 2020 08:36:56: 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 08:36:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.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 08:36:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:02: 5000000 INFO @ Tue, 16 Jun 2020 08:37:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:37:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:37:03: #1 total tags in treatment: 8956066 INFO @ Tue, 16 Jun 2020 08:37:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:03: #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 08:37:03: #1 tags after filtering in treatment: 8956066 INFO @ Tue, 16 Jun 2020 08:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:03: #2 number of paired peaks: 636 WARNING @ Tue, 16 Jun 2020 08:37:03: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:04: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 08:37:04: #2 alternative fragment length(s) may be 3,73 bps INFO @ Tue, 16 Jun 2020 08:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.05_model.r WARNING @ Tue, 16 Jun 2020 08:37:04: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:04: #2 You may need to consider one of the other alternative d(s): 3,73 WARNING @ Tue, 16 Jun 2020 08:37:04: #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 08:37:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:06: 1000000 INFO @ Tue, 16 Jun 2020 08:37:09: 6000000 INFO @ Tue, 16 Jun 2020 08:37:14: 2000000 INFO @ Tue, 16 Jun 2020 08:37:15: 7000000 INFO @ Tue, 16 Jun 2020 08:37:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:22: 3000000 INFO @ Tue, 16 Jun 2020 08:37:22: 8000000 INFO @ Tue, 16 Jun 2020 08:37:28: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:37:28: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:37:28: #1 total tags in treatment: 8956066 INFO @ Tue, 16 Jun 2020 08:37:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:28: #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 08:37:29: #1 tags after filtering in treatment: 8956066 INFO @ Tue, 16 Jun 2020 08:37:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:29: #2 number of paired peaks: 636 WARNING @ Tue, 16 Jun 2020 08:37:29: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:29: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 08:37:29: #2 alternative fragment length(s) may be 3,73 bps INFO @ Tue, 16 Jun 2020 08:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.10_model.r WARNING @ Tue, 16 Jun 2020 08:37:29: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:37:29: #2 You may need to consider one of the other alternative d(s): 3,73 WARNING @ Tue, 16 Jun 2020 08:37:29: #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 08:37:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:30: 4000000 INFO @ Tue, 16 Jun 2020 08:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1052 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:37: 5000000 INFO @ Tue, 16 Jun 2020 08:37:44: 6000000 INFO @ Tue, 16 Jun 2020 08:37:47: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:52: 7000000 INFO @ Tue, 16 Jun 2020 08:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (561 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:59: 8000000 INFO @ Tue, 16 Jun 2020 08:38:06: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:38:06: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:38:06: #1 total tags in treatment: 8956066 INFO @ Tue, 16 Jun 2020 08:38:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:06: #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 08:38:06: #1 tags after filtering in treatment: 8956066 INFO @ Tue, 16 Jun 2020 08:38:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:07: #2 number of paired peaks: 636 WARNING @ Tue, 16 Jun 2020 08:38:07: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:07: #2 predicted fragment length is 73 bps INFO @ Tue, 16 Jun 2020 08:38:07: #2 alternative fragment length(s) may be 3,73 bps INFO @ Tue, 16 Jun 2020 08:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.20_model.r WARNING @ Tue, 16 Jun 2020 08:38:07: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:07: #2 You may need to consider one of the other alternative d(s): 3,73 WARNING @ Tue, 16 Jun 2020 08:38:07: #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 08:38:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330988/SRX330988.20_summits.bed INFO @ Tue, 16 Jun 2020 08:38:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (366 records, 4 fields): 1 millis CompletedMACS2peakCalling