Job ID = 6497454 SRX = SRX494951 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:39:50 prefetch.2.10.7: 1) Downloading 'SRR1198483'... 2020-06-25T22:39:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:41:28 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:41:28 prefetch.2.10.7: 'SRR1198483' is valid 2020-06-25T22:41:28 prefetch.2.10.7: 1) 'SRR1198483' was downloaded successfully Read 13129788 spots for SRR1198483/SRR1198483.sra Written 13129788 spots for SRR1198483/SRR1198483.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: 00:03:09 13129788 reads; of these: 13129788 (100.00%) were unpaired; of these: 270394 (2.06%) aligned 0 times 10628351 (80.95%) aligned exactly 1 time 2231043 (16.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 2051401 / 12859394 = 0.1595 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 07:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.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 07:48:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:48:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:48:33: 1000000 INFO @ Fri, 26 Jun 2020 07:48:40: 2000000 INFO @ Fri, 26 Jun 2020 07:48:46: 3000000 INFO @ Fri, 26 Jun 2020 07:48:52: 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 @ Fri, 26 Jun 2020 07:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.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 07:48:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:48:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:48:58: 5000000 INFO @ Fri, 26 Jun 2020 07:49:03: 1000000 INFO @ Fri, 26 Jun 2020 07:49:05: 6000000 INFO @ Fri, 26 Jun 2020 07:49:10: 2000000 INFO @ Fri, 26 Jun 2020 07:49:11: 7000000 INFO @ Fri, 26 Jun 2020 07:49:17: 3000000 INFO @ Fri, 26 Jun 2020 07:49:18: 8000000 INFO @ Fri, 26 Jun 2020 07:49:24: 4000000 INFO @ Fri, 26 Jun 2020 07:49:24: 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 @ Fri, 26 Jun 2020 07:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.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 07:49:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:49:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:49:30: 5000000 INFO @ Fri, 26 Jun 2020 07:49:30: 10000000 INFO @ Fri, 26 Jun 2020 07:49:34: 1000000 INFO @ Fri, 26 Jun 2020 07:49:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:49:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:49:36: #1 total tags in treatment: 10807993 INFO @ Fri, 26 Jun 2020 07:49:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:49:36: #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 07:49:36: #1 tags after filtering in treatment: 10807993 INFO @ Fri, 26 Jun 2020 07:49:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:49:36: #1 finished! INFO @ Fri, 26 Jun 2020 07:49:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:49:37: #2 number of paired peaks: 364 WARNING @ Fri, 26 Jun 2020 07:49:37: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Fri, 26 Jun 2020 07:49:37: start model_add_line... INFO @ Fri, 26 Jun 2020 07:49:37: 6000000 INFO @ Fri, 26 Jun 2020 07:49:37: start X-correlation... INFO @ Fri, 26 Jun 2020 07:49:37: end of X-cor INFO @ Fri, 26 Jun 2020 07:49:37: #2 finished! INFO @ Fri, 26 Jun 2020 07:49:37: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 07:49:37: #2 alternative fragment length(s) may be 2,46 bps INFO @ Fri, 26 Jun 2020 07:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.05_model.r WARNING @ Fri, 26 Jun 2020 07:49:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:49:37: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Fri, 26 Jun 2020 07:49:37: #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 07:49:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:49:40: 2000000 INFO @ Fri, 26 Jun 2020 07:49:43: 7000000 INFO @ Fri, 26 Jun 2020 07:49:47: 3000000 INFO @ Fri, 26 Jun 2020 07:49:50: 8000000 INFO @ Fri, 26 Jun 2020 07:49:54: 4000000 INFO @ Fri, 26 Jun 2020 07:49:56: 9000000 INFO @ Fri, 26 Jun 2020 07:50:00: 5000000 INFO @ Fri, 26 Jun 2020 07:50:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:50:03: 10000000 INFO @ Fri, 26 Jun 2020 07:50:06: 6000000 INFO @ Fri, 26 Jun 2020 07:50:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:50:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:50:08: #1 total tags in treatment: 10807993 INFO @ Fri, 26 Jun 2020 07:50:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:50:08: #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 07:50:08: #1 tags after filtering in treatment: 10807993 INFO @ Fri, 26 Jun 2020 07:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:50:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:50:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:50:09: #2 number of paired peaks: 364 WARNING @ Fri, 26 Jun 2020 07:50:09: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Fri, 26 Jun 2020 07:50:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:50:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:50:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:50:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:50:09: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 07:50:09: #2 alternative fragment length(s) may be 2,46 bps INFO @ Fri, 26 Jun 2020 07:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.10_model.r WARNING @ Fri, 26 Jun 2020 07:50:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:50:09: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Fri, 26 Jun 2020 07:50:09: #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 07:50:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:50:13: 7000000 INFO @ Fri, 26 Jun 2020 07:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.05_summits.bed INFO @ Fri, 26 Jun 2020 07:50:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:50:19: 8000000 INFO @ Fri, 26 Jun 2020 07:50:24: 9000000 INFO @ Fri, 26 Jun 2020 07:50:30: 10000000 INFO @ Fri, 26 Jun 2020 07:50:32: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:50:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:50:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:50:35: #1 total tags in treatment: 10807993 INFO @ Fri, 26 Jun 2020 07:50:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:50:35: #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 07:50:35: #1 tags after filtering in treatment: 10807993 INFO @ Fri, 26 Jun 2020 07:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:50:35: #1 finished! INFO @ Fri, 26 Jun 2020 07:50:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:50:36: #2 number of paired peaks: 364 WARNING @ Fri, 26 Jun 2020 07:50:36: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Fri, 26 Jun 2020 07:50:36: start model_add_line... INFO @ Fri, 26 Jun 2020 07:50:36: start X-correlation... INFO @ Fri, 26 Jun 2020 07:50:36: end of X-cor INFO @ Fri, 26 Jun 2020 07:50:36: #2 finished! INFO @ Fri, 26 Jun 2020 07:50:36: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 07:50:36: #2 alternative fragment length(s) may be 2,46 bps INFO @ Fri, 26 Jun 2020 07:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.20_model.r WARNING @ Fri, 26 Jun 2020 07:50:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:50:36: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Fri, 26 Jun 2020 07:50:36: #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 07:50:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.10_summits.bed INFO @ Fri, 26 Jun 2020 07:50:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:51:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:51:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:51:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:51:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494951/SRX494951.20_summits.bed INFO @ Fri, 26 Jun 2020 07:51:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling