Job ID = 6367587 SRX = SRX331344 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:20 prefetch.2.10.7: 1) Downloading 'SRR947581'... 2020-06-15T23:29:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:08 prefetch.2.10.7: 1) 'SRR947581' was downloaded successfully Read 30577412 spots for SRR947581/SRR947581.sra Written 30577412 spots for SRR947581/SRR947581.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: 00:05:24 30577412 reads; of these: 30577412 (100.00%) were unpaired; of these: 2071836 (6.78%) aligned 0 times 22340435 (73.06%) aligned exactly 1 time 6165141 (20.16%) aligned >1 times 93.22% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 19013046 / 28505576 = 0.6670 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 08:44:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.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 08:44:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:22: 1000000 INFO @ Tue, 16 Jun 2020 08:44:26: 2000000 INFO @ Tue, 16 Jun 2020 08:44:31: 3000000 INFO @ Tue, 16 Jun 2020 08:44:35: 4000000 INFO @ Tue, 16 Jun 2020 08:44:39: 5000000 INFO @ Tue, 16 Jun 2020 08:44:44: 6000000 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 08:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.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 08:44:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:48: 7000000 INFO @ Tue, 16 Jun 2020 08:44:52: 1000000 INFO @ Tue, 16 Jun 2020 08:44:53: 8000000 INFO @ Tue, 16 Jun 2020 08:44:56: 2000000 INFO @ Tue, 16 Jun 2020 08:44:57: 9000000 INFO @ Tue, 16 Jun 2020 08:45:00: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:45:00: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:45:00: #1 total tags in treatment: 9492530 INFO @ Tue, 16 Jun 2020 08:45:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:00: #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 08:45:00: #1 tags after filtering in treatment: 9492530 INFO @ Tue, 16 Jun 2020 08:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:01: #2 number of paired peaks: 1327 INFO @ Tue, 16 Jun 2020 08:45:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:01: 3000000 INFO @ Tue, 16 Jun 2020 08:45:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:01: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:45:01: #2 alternative fragment length(s) may be 3,44,566 bps INFO @ Tue, 16 Jun 2020 08:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.05_model.r WARNING @ Tue, 16 Jun 2020 08:45:01: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:01: #2 You may need to consider one of the other alternative d(s): 3,44,566 WARNING @ Tue, 16 Jun 2020 08:45:01: #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 08:45:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:05: 4000000 INFO @ Tue, 16 Jun 2020 08:45:09: 5000000 INFO @ Tue, 16 Jun 2020 08:45:14: 6000000 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 08:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.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 08:45:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:18: 7000000 INFO @ Tue, 16 Jun 2020 08:45:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:23: 8000000 INFO @ Tue, 16 Jun 2020 08:45:23: 1000000 INFO @ Tue, 16 Jun 2020 08:45:27: 9000000 INFO @ Tue, 16 Jun 2020 08:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4325 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:29: 2000000 INFO @ Tue, 16 Jun 2020 08:45:30: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:45:30: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:45:30: #1 total tags in treatment: 9492530 INFO @ Tue, 16 Jun 2020 08:45:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:30: #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 08:45:30: #1 tags after filtering in treatment: 9492530 INFO @ Tue, 16 Jun 2020 08:45:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:31: #2 number of paired peaks: 1327 INFO @ Tue, 16 Jun 2020 08:45:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:31: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:45:31: #2 alternative fragment length(s) may be 3,44,566 bps INFO @ Tue, 16 Jun 2020 08:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.10_model.r WARNING @ Tue, 16 Jun 2020 08:45:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:31: #2 You may need to consider one of the other alternative d(s): 3,44,566 WARNING @ Tue, 16 Jun 2020 08:45:31: #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 08:45:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:35: 3000000 INFO @ Tue, 16 Jun 2020 08:45:40: 4000000 INFO @ Tue, 16 Jun 2020 08:45:46: 5000000 INFO @ Tue, 16 Jun 2020 08:45:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:57: 7000000 INFO @ Tue, 16 Jun 2020 08:46:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1699 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:03: 8000000 INFO @ Tue, 16 Jun 2020 08:46:09: 9000000 INFO @ Tue, 16 Jun 2020 08:46:12: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:46:12: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:46:12: #1 total tags in treatment: 9492530 INFO @ Tue, 16 Jun 2020 08:46:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:12: #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 08:46:12: #1 tags after filtering in treatment: 9492530 INFO @ Tue, 16 Jun 2020 08:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:13: #2 number of paired peaks: 1327 INFO @ Tue, 16 Jun 2020 08:46:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:13: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:46:13: #2 alternative fragment length(s) may be 3,44,566 bps INFO @ Tue, 16 Jun 2020 08:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.20_model.r WARNING @ Tue, 16 Jun 2020 08:46:13: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:13: #2 You may need to consider one of the other alternative d(s): 3,44,566 WARNING @ Tue, 16 Jun 2020 08:46:13: #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 08:46:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331344/SRX331344.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 1 millis CompletedMACS2peakCalling