Job ID = 6367480 SRX = SRX331237 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:21 prefetch.2.10.7: 1) Downloading 'SRR947469'... 2020-06-15T23:27:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:28:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:28:01 prefetch.2.10.7: 'SRR947469' is valid 2020-06-15T23:28:01 prefetch.2.10.7: 1) 'SRR947469' was downloaded successfully Read 6990390 spots for SRR947469/SRR947469.sra Written 6990390 spots for SRR947469/SRR947469.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: 00:01:06 6990390 reads; of these: 6990390 (100.00%) were unpaired; of these: 180928 (2.59%) aligned 0 times 5700642 (81.55%) aligned exactly 1 time 1108820 (15.86%) aligned >1 times 97.41% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 961608 / 6809462 = 0.1412 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 08:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.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 08:31:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:17: 1000000 INFO @ Tue, 16 Jun 2020 08:31:22: 2000000 INFO @ Tue, 16 Jun 2020 08:31:28: 3000000 INFO @ Tue, 16 Jun 2020 08:31:34: 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 @ Tue, 16 Jun 2020 08:31:39: 5000000 INFO @ Tue, 16 Jun 2020 08:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.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 08:31:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:44: #1 total tags in treatment: 5847854 INFO @ Tue, 16 Jun 2020 08:31:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:44: #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 08:31:44: #1 tags after filtering in treatment: 5847854 INFO @ Tue, 16 Jun 2020 08:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:45: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:31:45: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:45: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:31:45: #2 alternative fragment length(s) may be 2,33,541,586,597 bps INFO @ Tue, 16 Jun 2020 08:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:45: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:45: #2 You may need to consider one of the other alternative d(s): 2,33,541,586,597 WARNING @ Tue, 16 Jun 2020 08:31:45: #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 08:31:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:46: 1000000 INFO @ Tue, 16 Jun 2020 08:31:51: 2000000 INFO @ Tue, 16 Jun 2020 08:31:56: 3000000 INFO @ Tue, 16 Jun 2020 08:31:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:01: 4000000 INFO @ Tue, 16 Jun 2020 08:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (383 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:06: 5000000 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 08:32:10: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:10: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:10: #1 total tags in treatment: 5847854 INFO @ Tue, 16 Jun 2020 08:32:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:10: #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 08:32:10: #1 tags after filtering in treatment: 5847854 INFO @ Tue, 16 Jun 2020 08:32:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:11: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:32:11: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:11: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:32:11: #2 alternative fragment length(s) may be 2,33,541,586,597 bps INFO @ Tue, 16 Jun 2020 08:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:11: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:11: #2 You may need to consider one of the other alternative d(s): 2,33,541,586,597 WARNING @ Tue, 16 Jun 2020 08:32:11: #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 08:32:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.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 08:32:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:15: 1000000 INFO @ Tue, 16 Jun 2020 08:32:20: 2000000 INFO @ Tue, 16 Jun 2020 08:32:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:25: 3000000 INFO @ Tue, 16 Jun 2020 08:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.10_summits.bed INFO @ Tue, 16 Jun 2020 08:32:29: Done! INFO @ Tue, 16 Jun 2020 08:32:30: 4000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:35: 5000000 INFO @ Tue, 16 Jun 2020 08:32:39: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:39: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:39: #1 total tags in treatment: 5847854 INFO @ Tue, 16 Jun 2020 08:32:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:39: #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 08:32:39: #1 tags after filtering in treatment: 5847854 INFO @ Tue, 16 Jun 2020 08:32:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:39: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 08:32:39: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:39: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:32:39: #2 alternative fragment length(s) may be 2,33,541,586,597 bps INFO @ Tue, 16 Jun 2020 08:32:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.20_model.r WARNING @ Tue, 16 Jun 2020 08:32:39: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:39: #2 You may need to consider one of the other alternative d(s): 2,33,541,586,597 WARNING @ Tue, 16 Jun 2020 08:32:39: #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 08:32:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331237/SRX331237.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (21 records, 4 fields): 1 millis CompletedMACS2peakCalling