Job ID = 6497458 SRX = SRX494959 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:07:04 prefetch.2.10.7: 1) Downloading 'SRR1198491'... 2020-06-25T22:07:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:09:44 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:09:45 prefetch.2.10.7: 'SRR1198491' is valid 2020-06-25T22:09:45 prefetch.2.10.7: 1) 'SRR1198491' was downloaded successfully Read 14315583 spots for SRR1198491/SRR1198491.sra Written 14315583 spots for SRR1198491/SRR1198491.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:35 14315583 reads; of these: 14315583 (100.00%) were unpaired; of these: 295407 (2.06%) aligned 0 times 11731499 (81.95%) aligned exactly 1 time 2288677 (15.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 4768609 / 14020176 = 0.3401 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 07:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.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 07:17:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:18: 1000000 INFO @ Fri, 26 Jun 2020 07:17:23: 2000000 INFO @ Fri, 26 Jun 2020 07:17:29: 3000000 INFO @ Fri, 26 Jun 2020 07:17:34: 4000000 INFO @ Fri, 26 Jun 2020 07:17:39: 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 07:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.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 07:17:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:45: 6000000 INFO @ Fri, 26 Jun 2020 07:17:49: 1000000 INFO @ Fri, 26 Jun 2020 07:17:51: 7000000 INFO @ Fri, 26 Jun 2020 07:17:56: 2000000 INFO @ Fri, 26 Jun 2020 07:17:56: 8000000 INFO @ Fri, 26 Jun 2020 07:18:02: 9000000 INFO @ Fri, 26 Jun 2020 07:18:03: 3000000 INFO @ Fri, 26 Jun 2020 07:18:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:18:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:18:03: #1 total tags in treatment: 9251567 INFO @ Fri, 26 Jun 2020 07:18:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:18:03: #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 07:18:04: #1 tags after filtering in treatment: 9251567 INFO @ Fri, 26 Jun 2020 07:18:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:18:04: #1 finished! INFO @ Fri, 26 Jun 2020 07:18:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:18:04: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 07:18:04: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 07:18:04: start model_add_line... INFO @ Fri, 26 Jun 2020 07:18:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:18:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:18:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:18:04: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:18:04: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 07:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.05_model.r WARNING @ Fri, 26 Jun 2020 07:18:04: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:18:04: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 07:18:04: #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 07:18:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:18:10: 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 07:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.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 07:18:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:18:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:18:17: 5000000 INFO @ Fri, 26 Jun 2020 07:18:19: 1000000 INFO @ Fri, 26 Jun 2020 07:18:24: 6000000 INFO @ Fri, 26 Jun 2020 07:18:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:18:26: 2000000 INFO @ Fri, 26 Jun 2020 07:18:31: 7000000 INFO @ Fri, 26 Jun 2020 07:18:33: 3000000 INFO @ Fri, 26 Jun 2020 07:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.05_summits.bed INFO @ Fri, 26 Jun 2020 07:18:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:18:37: 8000000 INFO @ Fri, 26 Jun 2020 07:18:39: 4000000 INFO @ Fri, 26 Jun 2020 07:18:44: 9000000 INFO @ Fri, 26 Jun 2020 07:18:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:18:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:18:45: #1 total tags in treatment: 9251567 INFO @ Fri, 26 Jun 2020 07:18:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:18:45: #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 07:18:45: #1 tags after filtering in treatment: 9251567 INFO @ Fri, 26 Jun 2020 07:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:18:45: #1 finished! INFO @ Fri, 26 Jun 2020 07:18:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:18:46: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 07:18:46: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 07:18:46: start model_add_line... INFO @ Fri, 26 Jun 2020 07:18:46: 5000000 INFO @ Fri, 26 Jun 2020 07:18:46: start X-correlation... INFO @ Fri, 26 Jun 2020 07:18:46: end of X-cor INFO @ Fri, 26 Jun 2020 07:18:46: #2 finished! INFO @ Fri, 26 Jun 2020 07:18:46: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:18:46: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 07:18:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.10_model.r WARNING @ Fri, 26 Jun 2020 07:18:46: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:18:46: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 07:18:46: #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 07:18:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:18:53: 6000000 INFO @ Fri, 26 Jun 2020 07:18:59: 7000000 INFO @ Fri, 26 Jun 2020 07:19:05: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:19:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:19:12: 9000000 INFO @ Fri, 26 Jun 2020 07:19:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:19:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:19:13: #1 total tags in treatment: 9251567 INFO @ Fri, 26 Jun 2020 07:19:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:13: #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 07:19:13: #1 tags after filtering in treatment: 9251567 INFO @ Fri, 26 Jun 2020 07:19:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:19:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:14: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 07:19:14: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 07:19:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:14: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 07:19:14: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 07:19:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.20_model.r WARNING @ Fri, 26 Jun 2020 07:19:14: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:19:14: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 07:19:14: #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 07:19:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.10_summits.bed INFO @ Fri, 26 Jun 2020 07:19:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (473 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:19:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:19:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:19:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:19:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494959/SRX494959.20_summits.bed INFO @ Fri, 26 Jun 2020 07:19:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling