Job ID = 6367600 SRX = SRX331357 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR947594'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:37:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:37:08 prefetch.2.10.7: 1) 'SRR947594' was downloaded successfully Read 18812743 spots for SRR947594/SRR947594.sra Written 18812743 spots for SRR947594/SRR947594.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: 00:04:27 18812743 reads; of these: 18812743 (100.00%) were unpaired; of these: 149797 (0.80%) aligned 0 times 15591081 (82.88%) aligned exactly 1 time 3071865 (16.33%) aligned >1 times 99.20% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 8433368 / 18662946 = 0.4519 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 08:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.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 08:46:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:36: 1000000 INFO @ Tue, 16 Jun 2020 08:46:42: 2000000 INFO @ Tue, 16 Jun 2020 08:46:47: 3000000 INFO @ Tue, 16 Jun 2020 08:46:53: 4000000 INFO @ Tue, 16 Jun 2020 08:46:58: 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 @ Tue, 16 Jun 2020 08:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.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 08:47:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:05: 6000000 INFO @ Tue, 16 Jun 2020 08:47:08: 1000000 INFO @ Tue, 16 Jun 2020 08:47:11: 7000000 INFO @ Tue, 16 Jun 2020 08:47:15: 2000000 INFO @ Tue, 16 Jun 2020 08:47:18: 8000000 INFO @ Tue, 16 Jun 2020 08:47:21: 3000000 INFO @ Tue, 16 Jun 2020 08:47:24: 9000000 INFO @ Tue, 16 Jun 2020 08:47:28: 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 @ Tue, 16 Jun 2020 08:47:30: 10000000 INFO @ Tue, 16 Jun 2020 08:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.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 08:47:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:32: #1 total tags in treatment: 10229578 INFO @ Tue, 16 Jun 2020 08:47:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:32: #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 08:47:32: #1 tags after filtering in treatment: 10229578 INFO @ Tue, 16 Jun 2020 08:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:33: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 08:47:33: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:33: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:47:33: #2 alternative fragment length(s) may be 1,48,519,543,550 bps INFO @ Tue, 16 Jun 2020 08:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.05_model.r WARNING @ Tue, 16 Jun 2020 08:47:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:33: #2 You may need to consider one of the other alternative d(s): 1,48,519,543,550 WARNING @ Tue, 16 Jun 2020 08:47:33: #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 08:47:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:35: 5000000 INFO @ Tue, 16 Jun 2020 08:47:38: 1000000 INFO @ Tue, 16 Jun 2020 08:47:42: 6000000 INFO @ Tue, 16 Jun 2020 08:47:44: 2000000 INFO @ Tue, 16 Jun 2020 08:47:48: 7000000 INFO @ Tue, 16 Jun 2020 08:47:50: 3000000 INFO @ Tue, 16 Jun 2020 08:47:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:55: 8000000 INFO @ Tue, 16 Jun 2020 08:47:57: 4000000 INFO @ Tue, 16 Jun 2020 08:48:02: 9000000 INFO @ Tue, 16 Jun 2020 08:48:03: 5000000 INFO @ Tue, 16 Jun 2020 08:48:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (752 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:09: 10000000 INFO @ Tue, 16 Jun 2020 08:48:09: 6000000 INFO @ Tue, 16 Jun 2020 08:48:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:11: #1 total tags in treatment: 10229578 INFO @ Tue, 16 Jun 2020 08:48:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:11: #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 08:48:11: #1 tags after filtering in treatment: 10229578 INFO @ Tue, 16 Jun 2020 08:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:12: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 08:48:12: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:12: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:48:12: #2 alternative fragment length(s) may be 1,48,519,543,550 bps INFO @ Tue, 16 Jun 2020 08:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:12: #2 You may need to consider one of the other alternative d(s): 1,48,519,543,550 WARNING @ Tue, 16 Jun 2020 08:48:12: #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 08:48:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:15: 7000000 INFO @ Tue, 16 Jun 2020 08:48:21: 8000000 INFO @ Tue, 16 Jun 2020 08:48:26: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:32: 10000000 INFO @ Tue, 16 Jun 2020 08:48:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:33: #1 total tags in treatment: 10229578 INFO @ Tue, 16 Jun 2020 08:48:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:33: #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 08:48:33: #1 tags after filtering in treatment: 10229578 INFO @ Tue, 16 Jun 2020 08:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:34: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 08:48:34: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:34: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:48:34: #2 alternative fragment length(s) may be 1,48,519,543,550 bps INFO @ Tue, 16 Jun 2020 08:48:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.20_model.r WARNING @ Tue, 16 Jun 2020 08:48:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:34: #2 You may need to consider one of the other alternative d(s): 1,48,519,543,550 WARNING @ Tue, 16 Jun 2020 08:48:34: #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 08:48:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331357/SRX331357.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling