Job ID = 6368723 SRX = SRX5402747 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T01:13:10 prefetch.2.10.7: 1) Downloading 'SRR8602981'... 2020-06-16T01:13:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T01:15:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T01:15:37 prefetch.2.10.7: 1) 'SRR8602981' was downloaded successfully Read 32212115 spots for SRR8602981/SRR8602981.sra Written 32212115 spots for SRR8602981/SRR8602981.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: 00:07:34 32212115 reads; of these: 32212115 (100.00%) were unpaired; of these: 7760885 (24.09%) aligned 0 times 12601000 (39.12%) aligned exactly 1 time 11850230 (36.79%) aligned >1 times 75.91% overall alignment rate Time searching: 00:07:34 Overall time: 00:07:34 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] 9376482 / 24451230 = 0.3835 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 10:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.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 10:30:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:08: 1000000 INFO @ Tue, 16 Jun 2020 10:30:14: 2000000 INFO @ Tue, 16 Jun 2020 10:30:21: 3000000 INFO @ Tue, 16 Jun 2020 10:30:27: 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 10:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.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 10:30:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:34: 5000000 INFO @ Tue, 16 Jun 2020 10:30:40: 1000000 INFO @ Tue, 16 Jun 2020 10:30:42: 6000000 INFO @ Tue, 16 Jun 2020 10:30:49: 2000000 INFO @ Tue, 16 Jun 2020 10:30:50: 7000000 INFO @ Tue, 16 Jun 2020 10:30:58: 3000000 INFO @ Tue, 16 Jun 2020 10:30:58: 8000000 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 10:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.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 10:31:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:31:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:31:06: 9000000 INFO @ Tue, 16 Jun 2020 10:31:06: 4000000 INFO @ Tue, 16 Jun 2020 10:31:10: 1000000 INFO @ Tue, 16 Jun 2020 10:31:14: 10000000 INFO @ Tue, 16 Jun 2020 10:31:15: 5000000 INFO @ Tue, 16 Jun 2020 10:31:18: 2000000 INFO @ Tue, 16 Jun 2020 10:31:22: 11000000 INFO @ Tue, 16 Jun 2020 10:31:24: 6000000 INFO @ Tue, 16 Jun 2020 10:31:27: 3000000 INFO @ Tue, 16 Jun 2020 10:31:30: 12000000 INFO @ Tue, 16 Jun 2020 10:31:33: 7000000 INFO @ Tue, 16 Jun 2020 10:31:35: 4000000 INFO @ Tue, 16 Jun 2020 10:31:39: 13000000 INFO @ Tue, 16 Jun 2020 10:31:41: 8000000 INFO @ Tue, 16 Jun 2020 10:31:44: 5000000 INFO @ Tue, 16 Jun 2020 10:31:47: 14000000 INFO @ Tue, 16 Jun 2020 10:31:50: 9000000 INFO @ Tue, 16 Jun 2020 10:31:52: 6000000 INFO @ Tue, 16 Jun 2020 10:31:55: 15000000 INFO @ Tue, 16 Jun 2020 10:31:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:31:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:31:55: #1 total tags in treatment: 15074748 INFO @ Tue, 16 Jun 2020 10:31:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:31:55: #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 10:31:56: #1 tags after filtering in treatment: 15074748 INFO @ Tue, 16 Jun 2020 10:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:31:56: #1 finished! INFO @ Tue, 16 Jun 2020 10:31:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:31:57: #2 number of paired peaks: 3122 INFO @ Tue, 16 Jun 2020 10:31:57: start model_add_line... INFO @ Tue, 16 Jun 2020 10:31:57: start X-correlation... INFO @ Tue, 16 Jun 2020 10:31:57: end of X-cor INFO @ Tue, 16 Jun 2020 10:31:57: #2 finished! INFO @ Tue, 16 Jun 2020 10:31:57: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 10:31:57: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 16 Jun 2020 10:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.05_model.r WARNING @ Tue, 16 Jun 2020 10:31:57: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:31:57: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 16 Jun 2020 10:31:57: #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 10:31:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:31:59: 10000000 INFO @ Tue, 16 Jun 2020 10:32:00: 7000000 INFO @ Tue, 16 Jun 2020 10:32:07: 11000000 INFO @ Tue, 16 Jun 2020 10:32:08: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:32:15: 12000000 INFO @ Tue, 16 Jun 2020 10:32:15: 9000000 INFO @ Tue, 16 Jun 2020 10:32:23: 10000000 INFO @ Tue, 16 Jun 2020 10:32:23: 13000000 INFO @ Tue, 16 Jun 2020 10:32:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:32:30: 11000000 INFO @ Tue, 16 Jun 2020 10:32:31: 14000000 INFO @ Tue, 16 Jun 2020 10:32:38: 12000000 INFO @ Tue, 16 Jun 2020 10:32:40: 15000000 INFO @ Tue, 16 Jun 2020 10:32:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:32:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:32:40: #1 total tags in treatment: 15074748 INFO @ Tue, 16 Jun 2020 10:32:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:32:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:32:40: #1 tags after filtering in treatment: 15074748 INFO @ Tue, 16 Jun 2020 10:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:32:40: #1 finished! INFO @ Tue, 16 Jun 2020 10:32:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:32:42: #2 number of paired peaks: 3122 INFO @ Tue, 16 Jun 2020 10:32:42: start model_add_line... INFO @ Tue, 16 Jun 2020 10:32:42: start X-correlation... INFO @ Tue, 16 Jun 2020 10:32:42: end of X-cor INFO @ Tue, 16 Jun 2020 10:32:42: #2 finished! INFO @ Tue, 16 Jun 2020 10:32:42: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 10:32:42: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 16 Jun 2020 10:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.10_model.r WARNING @ Tue, 16 Jun 2020 10:32:42: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:32:42: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 16 Jun 2020 10:32:42: #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 10:32:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:32:45: 13000000 INFO @ Tue, 16 Jun 2020 10:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.05_summits.bed INFO @ Tue, 16 Jun 2020 10:32:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (11868 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:32:51: 14000000 INFO @ Tue, 16 Jun 2020 10:32:58: 15000000 INFO @ Tue, 16 Jun 2020 10:32:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:32:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:32:58: #1 total tags in treatment: 15074748 INFO @ Tue, 16 Jun 2020 10:32:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:32:58: #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 10:32:58: #1 tags after filtering in treatment: 15074748 INFO @ Tue, 16 Jun 2020 10:32:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:32:58: #1 finished! INFO @ Tue, 16 Jun 2020 10:32:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:33:00: #2 number of paired peaks: 3122 INFO @ Tue, 16 Jun 2020 10:33:00: start model_add_line... INFO @ Tue, 16 Jun 2020 10:33:00: start X-correlation... INFO @ Tue, 16 Jun 2020 10:33:00: end of X-cor INFO @ Tue, 16 Jun 2020 10:33:00: #2 finished! INFO @ Tue, 16 Jun 2020 10:33:00: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 10:33:00: #2 alternative fragment length(s) may be 4,67 bps INFO @ Tue, 16 Jun 2020 10:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.20_model.r WARNING @ Tue, 16 Jun 2020 10:33:00: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:33:00: #2 You may need to consider one of the other alternative d(s): 4,67 WARNING @ Tue, 16 Jun 2020 10:33:00: #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 10:33:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:33:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:33:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:33:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.10_summits.bed INFO @ Tue, 16 Jun 2020 10:33:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7894 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:33:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402747/SRX5402747.20_summits.bed INFO @ Tue, 16 Jun 2020 10:33:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3712 records, 4 fields): 5 millis CompletedMACS2peakCalling