Job ID = 6368721 SRX = SRX5402745 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:50 prefetch.2.10.7: 1) Downloading 'SRR8602979'... 2020-06-16T00:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:38:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:38:36 prefetch.2.10.7: 1) 'SRR8602979' was downloaded successfully Read 35003294 spots for SRR8602979/SRR8602979.sra Written 35003294 spots for SRR8602979/SRR8602979.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: 00:07:12 35003294 reads; of these: 35003294 (100.00%) were unpaired; of these: 11383842 (32.52%) aligned 0 times 13693155 (39.12%) aligned exactly 1 time 9926297 (28.36%) aligned >1 times 67.48% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 7453072 / 23619452 = 0.3155 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 09:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.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 09:52:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:53: 1000000 INFO @ Tue, 16 Jun 2020 09:52:59: 2000000 INFO @ Tue, 16 Jun 2020 09:53:05: 3000000 INFO @ Tue, 16 Jun 2020 09:53:11: 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 09:53:17: 5000000 INFO @ Tue, 16 Jun 2020 09:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.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 09:53:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:23: 1000000 INFO @ Tue, 16 Jun 2020 09:53:23: 6000000 INFO @ Tue, 16 Jun 2020 09:53:28: 2000000 INFO @ Tue, 16 Jun 2020 09:53:29: 7000000 INFO @ Tue, 16 Jun 2020 09:53:34: 3000000 INFO @ Tue, 16 Jun 2020 09:53:35: 8000000 INFO @ Tue, 16 Jun 2020 09:53:39: 4000000 INFO @ Tue, 16 Jun 2020 09:53:41: 9000000 INFO @ Tue, 16 Jun 2020 09:53:45: 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 09:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.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 09:53:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:48: 10000000 INFO @ Tue, 16 Jun 2020 09:53:50: 6000000 INFO @ Tue, 16 Jun 2020 09:53:53: 1000000 INFO @ Tue, 16 Jun 2020 09:53:54: 11000000 INFO @ Tue, 16 Jun 2020 09:53:56: 7000000 INFO @ Tue, 16 Jun 2020 09:53:59: 2000000 INFO @ Tue, 16 Jun 2020 09:54:00: 12000000 INFO @ Tue, 16 Jun 2020 09:54:01: 8000000 INFO @ Tue, 16 Jun 2020 09:54:05: 3000000 INFO @ Tue, 16 Jun 2020 09:54:07: 13000000 INFO @ Tue, 16 Jun 2020 09:54:07: 9000000 INFO @ Tue, 16 Jun 2020 09:54:11: 4000000 INFO @ Tue, 16 Jun 2020 09:54:12: 10000000 INFO @ Tue, 16 Jun 2020 09:54:13: 14000000 INFO @ Tue, 16 Jun 2020 09:54:17: 5000000 INFO @ Tue, 16 Jun 2020 09:54:18: 11000000 INFO @ Tue, 16 Jun 2020 09:54:20: 15000000 INFO @ Tue, 16 Jun 2020 09:54:23: 6000000 INFO @ Tue, 16 Jun 2020 09:54:24: 12000000 INFO @ Tue, 16 Jun 2020 09:54:26: 16000000 INFO @ Tue, 16 Jun 2020 09:54:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:27: #1 total tags in treatment: 16166380 INFO @ Tue, 16 Jun 2020 09:54:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:27: #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 09:54:27: #1 tags after filtering in treatment: 16166380 INFO @ Tue, 16 Jun 2020 09:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:29: #2 number of paired peaks: 1899 INFO @ Tue, 16 Jun 2020 09:54:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:29: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:54:29: #2 alternative fragment length(s) may be 4,78 bps INFO @ Tue, 16 Jun 2020 09:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.05_model.r WARNING @ Tue, 16 Jun 2020 09:54:29: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:29: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Tue, 16 Jun 2020 09:54:29: #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 09:54:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:29: 7000000 INFO @ Tue, 16 Jun 2020 09:54:29: 13000000 INFO @ Tue, 16 Jun 2020 09:54:35: 8000000 INFO @ Tue, 16 Jun 2020 09:54:35: 14000000 INFO @ Tue, 16 Jun 2020 09:54:41: 15000000 INFO @ Tue, 16 Jun 2020 09:54:41: 9000000 INFO @ Tue, 16 Jun 2020 09:54:46: 16000000 INFO @ Tue, 16 Jun 2020 09:54:47: 10000000 INFO @ Tue, 16 Jun 2020 09:54:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:47: #1 total tags in treatment: 16166380 INFO @ Tue, 16 Jun 2020 09:54:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:47: #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 09:54:47: #1 tags after filtering in treatment: 16166380 INFO @ Tue, 16 Jun 2020 09:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:49: #2 number of paired peaks: 1899 INFO @ Tue, 16 Jun 2020 09:54:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:49: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:54:49: #2 alternative fragment length(s) may be 4,78 bps INFO @ Tue, 16 Jun 2020 09:54:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:49: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:49: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Tue, 16 Jun 2020 09:54:49: #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 09:54:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:53: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:59: 12000000 INFO @ Tue, 16 Jun 2020 09:55:05: 13000000 INFO @ Tue, 16 Jun 2020 09:55:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:11: 14000000 INFO @ Tue, 16 Jun 2020 09:55:17: 15000000 INFO @ Tue, 16 Jun 2020 09:55:23: 16000000 INFO @ Tue, 16 Jun 2020 09:55:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:55:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:55:24: #1 total tags in treatment: 16166380 INFO @ Tue, 16 Jun 2020 09:55:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:24: #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 09:55:24: #1 tags after filtering in treatment: 16166380 INFO @ Tue, 16 Jun 2020 09:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:26: #2 number of paired peaks: 1899 INFO @ Tue, 16 Jun 2020 09:55:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:26: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:55:26: #2 alternative fragment length(s) may be 4,78 bps INFO @ Tue, 16 Jun 2020 09:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.20_model.r WARNING @ Tue, 16 Jun 2020 09:55:26: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:26: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Tue, 16 Jun 2020 09:55:26: #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 09:55:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.05_summits.bed INFO @ Tue, 16 Jun 2020 09:55:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10422 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6451 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402745/SRX5402745.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2890 records, 4 fields): 4 millis CompletedMACS2peakCalling