Job ID = 6507947 SRX = SRX495107 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:23:03 prefetch.2.10.7: 1) Downloading 'SRR1198639'... 2020-06-26T13:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:25:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:25:46 prefetch.2.10.7: 1) 'SRR1198639' was downloaded successfully Read 25622332 spots for SRR1198639/SRR1198639.sra Written 25622332 spots for SRR1198639/SRR1198639.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: 00:05:50 25622332 reads; of these: 25622332 (100.00%) were unpaired; of these: 3968772 (15.49%) aligned 0 times 16160913 (63.07%) aligned exactly 1 time 5492647 (21.44%) aligned >1 times 84.51% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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 12 files... [bam_rmdupse_core] 13089814 / 21653560 = 0.6045 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 22:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.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 22:37:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:30: 1000000 INFO @ Fri, 26 Jun 2020 22:37:38: 2000000 INFO @ Fri, 26 Jun 2020 22:37:46: 3000000 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 22:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.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 22:37:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:54: 4000000 INFO @ Fri, 26 Jun 2020 22:37:58: 1000000 INFO @ Fri, 26 Jun 2020 22:38:02: 5000000 INFO @ Fri, 26 Jun 2020 22:38:05: 2000000 INFO @ Fri, 26 Jun 2020 22:38:09: 6000000 INFO @ Fri, 26 Jun 2020 22:38:12: 3000000 INFO @ Fri, 26 Jun 2020 22:38:17: 7000000 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 22:38:19: 4000000 INFO @ Fri, 26 Jun 2020 22:38:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.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 22:38:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:38:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:38:25: 8000000 INFO @ Fri, 26 Jun 2020 22:38:26: 5000000 INFO @ Fri, 26 Jun 2020 22:38:27: 1000000 INFO @ Fri, 26 Jun 2020 22:38:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:38:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:38:29: #1 total tags in treatment: 8563746 INFO @ Fri, 26 Jun 2020 22:38:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:29: #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 22:38:29: #1 tags after filtering in treatment: 8563746 INFO @ Fri, 26 Jun 2020 22:38:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:29: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:29: #2 number of paired peaks: 688 WARNING @ Fri, 26 Jun 2020 22:38:29: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:29: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:29: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:30: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:30: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:30: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 22:38:30: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 22:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.05_model.r WARNING @ Fri, 26 Jun 2020 22:38:30: #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 22:38:30: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 22:38:30: #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 22:38:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:34: 6000000 INFO @ Fri, 26 Jun 2020 22:38:35: 2000000 INFO @ Fri, 26 Jun 2020 22:38:41: 7000000 INFO @ Fri, 26 Jun 2020 22:38:42: 3000000 INFO @ Fri, 26 Jun 2020 22:38:48: 8000000 INFO @ Fri, 26 Jun 2020 22:38:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:49: 4000000 INFO @ Fri, 26 Jun 2020 22:38:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:38:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:38:52: #1 total tags in treatment: 8563746 INFO @ Fri, 26 Jun 2020 22:38:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:52: #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 22:38:52: #1 tags after filtering in treatment: 8563746 INFO @ Fri, 26 Jun 2020 22:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:52: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:52: #2 number of paired peaks: 688 WARNING @ Fri, 26 Jun 2020 22:38:52: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:52: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:52: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:53: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:53: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:53: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 22:38:53: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 22:38:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.10_model.r WARNING @ Fri, 26 Jun 2020 22:38:53: #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 22:38:53: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 22:38:53: #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 22:38:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:56: 5000000 INFO @ Fri, 26 Jun 2020 22:38:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.05_summits.bed INFO @ Fri, 26 Jun 2020 22:38:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1315 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:39:03: 6000000 INFO @ Fri, 26 Jun 2020 22:39:09: 7000000 INFO @ Fri, 26 Jun 2020 22:39:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:16: 8000000 INFO @ Fri, 26 Jun 2020 22:39:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.10_summits.bed INFO @ Fri, 26 Jun 2020 22:39:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:39:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:39:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:39:20: #1 total tags in treatment: 8563746 INFO @ Fri, 26 Jun 2020 22:39:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:20: #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 22:39:20: #1 tags after filtering in treatment: 8563746 INFO @ Fri, 26 Jun 2020 22:39:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:20: #2 number of paired peaks: 688 WARNING @ Fri, 26 Jun 2020 22:39:20: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:20: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 22:39:20: #2 alternative fragment length(s) may be 2,48 bps INFO @ Fri, 26 Jun 2020 22:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.20_model.r WARNING @ Fri, 26 Jun 2020 22:39:20: #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 22:39:20: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Fri, 26 Jun 2020 22:39:20: #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 22:39:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:39:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495107/SRX495107.20_summits.bed INFO @ Fri, 26 Jun 2020 22:39:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling