Job ID = 6368539 SRX = SRX5020767 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:19:21 prefetch.2.10.7: 1) Downloading 'SRR8201390'... 2020-06-16T00:19:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:09 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:09 prefetch.2.10.7: 1) 'SRR8201390' was downloaded successfully Read 24711238 spots for SRR8201390/SRR8201390.sra Written 24711238 spots for SRR8201390/SRR8201390.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 24711238 reads; of these: 24711238 (100.00%) were unpaired; of these: 2022858 (8.19%) aligned 0 times 19223145 (77.79%) aligned exactly 1 time 3465235 (14.02%) aligned >1 times 91.81% 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 12 files... [bam_rmdupse_core] 9301923 / 22688380 = 0.4100 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 09:34:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.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 09:34:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:58: 1000000 INFO @ Tue, 16 Jun 2020 09:35:03: 2000000 INFO @ Tue, 16 Jun 2020 09:35:08: 3000000 INFO @ Tue, 16 Jun 2020 09:35:12: 4000000 INFO @ Tue, 16 Jun 2020 09:35:17: 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 09:35:22: 6000000 INFO @ Tue, 16 Jun 2020 09:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.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 09:35:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:27: 7000000 INFO @ Tue, 16 Jun 2020 09:35:29: 1000000 INFO @ Tue, 16 Jun 2020 09:35:32: 8000000 INFO @ Tue, 16 Jun 2020 09:35:35: 2000000 INFO @ Tue, 16 Jun 2020 09:35:37: 9000000 INFO @ Tue, 16 Jun 2020 09:35:41: 3000000 INFO @ Tue, 16 Jun 2020 09:35:42: 10000000 INFO @ Tue, 16 Jun 2020 09:35:46: 4000000 INFO @ Tue, 16 Jun 2020 09:35:47: 11000000 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 09:35:52: 5000000 INFO @ Tue, 16 Jun 2020 09:35:52: 12000000 INFO @ Tue, 16 Jun 2020 09:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.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 09:35:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:58: 13000000 INFO @ Tue, 16 Jun 2020 09:35:58: 6000000 INFO @ Tue, 16 Jun 2020 09:35:58: 1000000 INFO @ Tue, 16 Jun 2020 09:36:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:00: #1 total tags in treatment: 13386457 INFO @ Tue, 16 Jun 2020 09:36:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:00: #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 09:36:00: #1 tags after filtering in treatment: 13386457 INFO @ Tue, 16 Jun 2020 09:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:01: #2 number of paired peaks: 648 WARNING @ Tue, 16 Jun 2020 09:36:01: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:01: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 09:36:01: #2 alternative fragment length(s) may be 3,139 bps INFO @ Tue, 16 Jun 2020 09:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.05_model.r INFO @ Tue, 16 Jun 2020 09:36:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:03: 7000000 INFO @ Tue, 16 Jun 2020 09:36:04: 2000000 INFO @ Tue, 16 Jun 2020 09:36:09: 8000000 INFO @ Tue, 16 Jun 2020 09:36:10: 3000000 INFO @ Tue, 16 Jun 2020 09:36:14: 9000000 INFO @ Tue, 16 Jun 2020 09:36:16: 4000000 INFO @ Tue, 16 Jun 2020 09:36:20: 10000000 INFO @ Tue, 16 Jun 2020 09:36:21: 5000000 INFO @ Tue, 16 Jun 2020 09:36:26: 11000000 INFO @ Tue, 16 Jun 2020 09:36:27: 6000000 INFO @ Tue, 16 Jun 2020 09:36:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:31: 12000000 INFO @ Tue, 16 Jun 2020 09:36:33: 7000000 INFO @ Tue, 16 Jun 2020 09:36:37: 13000000 INFO @ Tue, 16 Jun 2020 09:36:38: 8000000 INFO @ Tue, 16 Jun 2020 09:36:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:40: #1 total tags in treatment: 13386457 INFO @ Tue, 16 Jun 2020 09:36:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:40: #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 09:36:40: #1 tags after filtering in treatment: 13386457 INFO @ Tue, 16 Jun 2020 09:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:41: #2 number of paired peaks: 648 WARNING @ Tue, 16 Jun 2020 09:36:41: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:41: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 09:36:41: #2 alternative fragment length(s) may be 3,139 bps INFO @ Tue, 16 Jun 2020 09:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.10_model.r INFO @ Tue, 16 Jun 2020 09:36:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2593 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:44: 9000000 INFO @ Tue, 16 Jun 2020 09:36:49: 10000000 INFO @ Tue, 16 Jun 2020 09:36:55: 11000000 INFO @ Tue, 16 Jun 2020 09:37:00: 12000000 INFO @ Tue, 16 Jun 2020 09:37:06: 13000000 INFO @ Tue, 16 Jun 2020 09:37:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:08: #1 total tags in treatment: 13386457 INFO @ Tue, 16 Jun 2020 09:37:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:08: #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 09:37:08: #1 tags after filtering in treatment: 13386457 INFO @ Tue, 16 Jun 2020 09:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:09: #2 number of paired peaks: 648 WARNING @ Tue, 16 Jun 2020 09:37:09: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:09: #2 predicted fragment length is 139 bps INFO @ Tue, 16 Jun 2020 09:37:09: #2 alternative fragment length(s) may be 3,139 bps INFO @ Tue, 16 Jun 2020 09:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.20_model.r INFO @ Tue, 16 Jun 2020 09:37:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020767/SRX5020767.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (494 records, 4 fields): 1 millis CompletedMACS2peakCalling