Job ID = 6367586 SRX = SRX331343 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:05 prefetch.2.10.7: 1) Downloading 'SRR947580'... 2020-06-15T23:29:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:09 prefetch.2.10.7: 'SRR947580' is valid 2020-06-15T23:32:09 prefetch.2.10.7: 1) 'SRR947580' was downloaded successfully Read 16994712 spots for SRR947580/SRR947580.sra Written 16994712 spots for SRR947580/SRR947580.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: 00:04:00 16994712 reads; of these: 16994712 (100.00%) were unpaired; of these: 905112 (5.33%) aligned 0 times 12502240 (73.57%) aligned exactly 1 time 3587360 (21.11%) aligned >1 times 94.67% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 7478477 / 16089600 = 0.4648 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 08:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.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 08:39:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:04: 1000000 INFO @ Tue, 16 Jun 2020 08:40:09: 2000000 INFO @ Tue, 16 Jun 2020 08:40:15: 3000000 INFO @ Tue, 16 Jun 2020 08:40:20: 4000000 INFO @ Tue, 16 Jun 2020 08:40:26: 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 08:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.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 08:40:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:31: 6000000 INFO @ Tue, 16 Jun 2020 08:40:33: 1000000 INFO @ Tue, 16 Jun 2020 08:40:37: 7000000 INFO @ Tue, 16 Jun 2020 08:40:38: 2000000 INFO @ Tue, 16 Jun 2020 08:40:42: 8000000 INFO @ Tue, 16 Jun 2020 08:40:43: 3000000 INFO @ Tue, 16 Jun 2020 08:40:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:45: #1 total tags in treatment: 8611123 INFO @ Tue, 16 Jun 2020 08:40:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:45: #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 08:40:46: #1 tags after filtering in treatment: 8611123 INFO @ Tue, 16 Jun 2020 08:40:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:46: #2 number of paired peaks: 1456 INFO @ Tue, 16 Jun 2020 08:40:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:46: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:40:46: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 16 Jun 2020 08:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.05_model.r WARNING @ Tue, 16 Jun 2020 08:40:46: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:46: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 16 Jun 2020 08:40:46: #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 08:40:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:48: 4000000 INFO @ Tue, 16 Jun 2020 08:40:52: 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 08:40:57: 6000000 INFO @ Tue, 16 Jun 2020 08:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.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 08:40:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:02: 7000000 INFO @ Tue, 16 Jun 2020 08:41:04: 1000000 INFO @ Tue, 16 Jun 2020 08:41:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:06: 8000000 INFO @ Tue, 16 Jun 2020 08:41:09: 2000000 INFO @ Tue, 16 Jun 2020 08:41:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:41:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:41:09: #1 total tags in treatment: 8611123 INFO @ Tue, 16 Jun 2020 08:41:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:09: #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 08:41:10: #1 tags after filtering in treatment: 8611123 INFO @ Tue, 16 Jun 2020 08:41:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:10: #2 number of paired peaks: 1456 INFO @ Tue, 16 Jun 2020 08:41:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:10: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:41:10: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 16 Jun 2020 08:41:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.10_model.r WARNING @ Tue, 16 Jun 2020 08:41:10: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:10: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 16 Jun 2020 08:41:10: #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 08:41:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:13: 3000000 INFO @ Tue, 16 Jun 2020 08:41:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4247 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:18: 4000000 INFO @ Tue, 16 Jun 2020 08:41:23: 5000000 INFO @ Tue, 16 Jun 2020 08:41:27: 6000000 INFO @ Tue, 16 Jun 2020 08:41:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:32: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:36: 8000000 INFO @ Tue, 16 Jun 2020 08:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2111 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:41:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:41:39: #1 total tags in treatment: 8611123 INFO @ Tue, 16 Jun 2020 08:41:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:39: #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 08:41:39: #1 tags after filtering in treatment: 8611123 INFO @ Tue, 16 Jun 2020 08:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:40: #2 number of paired peaks: 1456 INFO @ Tue, 16 Jun 2020 08:41:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:40: #2 predicted fragment length is 92 bps INFO @ Tue, 16 Jun 2020 08:41:40: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 16 Jun 2020 08:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.20_model.r WARNING @ Tue, 16 Jun 2020 08:41:40: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:40: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 16 Jun 2020 08:41:40: #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 08:41:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331343/SRX331343.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (794 records, 4 fields): 2 millis CompletedMACS2peakCalling