Job ID = 6497564 SRX = SRX743647 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:18:29 prefetch.2.10.7: 1) Downloading 'SRR1630862'... 2020-06-25T22:18:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:53 prefetch.2.10.7: 'SRR1630862' is valid 2020-06-25T22:19:53 prefetch.2.10.7: 1) 'SRR1630862' was downloaded successfully Read 10087884 spots for SRR1630862/SRR1630862.sra Written 10087884 spots for SRR1630862/SRR1630862.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: 00:02:37 10087884 reads; of these: 10087884 (100.00%) were unpaired; of these: 1447057 (14.34%) aligned 0 times 7313640 (72.50%) aligned exactly 1 time 1327187 (13.16%) aligned >1 times 85.66% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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_rmdupse_core] 923333 / 8640827 = 0.1069 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 07:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.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 07:27:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:24: 1000000 INFO @ Fri, 26 Jun 2020 07:27:31: 2000000 INFO @ Fri, 26 Jun 2020 07:27:37: 3000000 INFO @ Fri, 26 Jun 2020 07:27:43: 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 07:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.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 07:27:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:50: 5000000 INFO @ Fri, 26 Jun 2020 07:27:55: 1000000 INFO @ Fri, 26 Jun 2020 07:27:57: 6000000 INFO @ Fri, 26 Jun 2020 07:28:02: 2000000 INFO @ Fri, 26 Jun 2020 07:28:04: 7000000 INFO @ Fri, 26 Jun 2020 07:28:08: 3000000 INFO @ Fri, 26 Jun 2020 07:28:09: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:28:09: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:28:09: #1 total tags in treatment: 7717494 INFO @ Fri, 26 Jun 2020 07:28:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:09: #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 07:28:09: #1 tags after filtering in treatment: 7717494 INFO @ Fri, 26 Jun 2020 07:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:28:09: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:09: #2 number of paired peaks: 195 WARNING @ Fri, 26 Jun 2020 07:28:09: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:09: #2 predicted fragment length is 52 bps INFO @ Fri, 26 Jun 2020 07:28:09: #2 alternative fragment length(s) may be 1,52,472,505,529,536,584 bps INFO @ Fri, 26 Jun 2020 07:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.05_model.r WARNING @ Fri, 26 Jun 2020 07:28:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:28:09: #2 You may need to consider one of the other alternative d(s): 1,52,472,505,529,536,584 WARNING @ Fri, 26 Jun 2020 07:28:09: #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 07:28:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:15: 4000000 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 07:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.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 07:28:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:28:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:28:21: 5000000 INFO @ Fri, 26 Jun 2020 07:28:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:28:25: 1000000 INFO @ Fri, 26 Jun 2020 07:28:28: 6000000 INFO @ Fri, 26 Jun 2020 07:28:32: 2000000 INFO @ Fri, 26 Jun 2020 07:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.05_summits.bed INFO @ Fri, 26 Jun 2020 07:28:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:28:35: 7000000 INFO @ Fri, 26 Jun 2020 07:28:38: 3000000 INFO @ Fri, 26 Jun 2020 07:28:40: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:28:40: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:28:40: #1 total tags in treatment: 7717494 INFO @ Fri, 26 Jun 2020 07:28:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:40: #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 07:28:40: #1 tags after filtering in treatment: 7717494 INFO @ Fri, 26 Jun 2020 07:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:28:40: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:41: #2 number of paired peaks: 195 WARNING @ Fri, 26 Jun 2020 07:28:41: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:41: #2 predicted fragment length is 52 bps INFO @ Fri, 26 Jun 2020 07:28:41: #2 alternative fragment length(s) may be 1,52,472,505,529,536,584 bps INFO @ Fri, 26 Jun 2020 07:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.10_model.r WARNING @ Fri, 26 Jun 2020 07:28:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:28:41: #2 You may need to consider one of the other alternative d(s): 1,52,472,505,529,536,584 WARNING @ Fri, 26 Jun 2020 07:28:41: #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 07:28:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:45: 4000000 INFO @ Fri, 26 Jun 2020 07:28:52: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:28:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:28:59: 6000000 INFO @ Fri, 26 Jun 2020 07:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.10_summits.bed INFO @ Fri, 26 Jun 2020 07:29:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:29:06: 7000000 INFO @ Fri, 26 Jun 2020 07:29:10: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:29:10: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:29:10: #1 total tags in treatment: 7717494 INFO @ Fri, 26 Jun 2020 07:29:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:10: #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 07:29:11: #1 tags after filtering in treatment: 7717494 INFO @ Fri, 26 Jun 2020 07:29:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:29:11: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:11: #2 number of paired peaks: 195 WARNING @ Fri, 26 Jun 2020 07:29:11: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:11: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:11: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:11: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:11: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:11: #2 predicted fragment length is 52 bps INFO @ Fri, 26 Jun 2020 07:29:11: #2 alternative fragment length(s) may be 1,52,472,505,529,536,584 bps INFO @ Fri, 26 Jun 2020 07:29:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.20_model.r WARNING @ Fri, 26 Jun 2020 07:29:11: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:29:11: #2 You may need to consider one of the other alternative d(s): 1,52,472,505,529,536,584 WARNING @ Fri, 26 Jun 2020 07:29:11: #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 07:29:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:29:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743647/SRX743647.20_summits.bed INFO @ Fri, 26 Jun 2020 07:29:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling