Job ID = 6497490 SRX = SRX495011 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:22:00 prefetch.2.10.7: 1) Downloading 'SRR1198543'... 2020-06-25T22:22:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:23:28 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:23:28 prefetch.2.10.7: 'SRR1198543' is valid 2020-06-25T22:23:28 prefetch.2.10.7: 1) 'SRR1198543' was downloaded successfully Read 11801157 spots for SRR1198543/SRR1198543.sra Written 11801157 spots for SRR1198543/SRR1198543.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: 00:02:26 11801157 reads; of these: 11801157 (100.00%) were unpaired; of these: 1018600 (8.63%) aligned 0 times 8925626 (75.63%) aligned exactly 1 time 1856931 (15.74%) aligned >1 times 91.37% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 5965582 / 10782557 = 0.5533 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 @ Fri, 26 Jun 2020 07:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.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 @ Fri, 26 Jun 2020 07:29:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:29:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:29:31: 1000000 INFO @ Fri, 26 Jun 2020 07:29:36: 2000000 INFO @ Fri, 26 Jun 2020 07:29:41: 3000000 INFO @ Fri, 26 Jun 2020 07:29:47: 4000000 INFO @ Fri, 26 Jun 2020 07:29:51: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:29:51: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:29:51: #1 total tags in treatment: 4816975 INFO @ Fri, 26 Jun 2020 07:29:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:29:51: #1 tags after filtering in treatment: 4816975 INFO @ Fri, 26 Jun 2020 07:29:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:29:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:51: #2 number of paired peaks: 710 WARNING @ Fri, 26 Jun 2020 07:29:51: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:51: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:51: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:51: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:51: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:51: #2 predicted fragment length is 155 bps INFO @ Fri, 26 Jun 2020 07:29:51: #2 alternative fragment length(s) may be 138,155 bps INFO @ Fri, 26 Jun 2020 07:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.05_model.r INFO @ Fri, 26 Jun 2020 07:29:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:51: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.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 @ Fri, 26 Jun 2020 07:29:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:29:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:00: 1000000 INFO @ Fri, 26 Jun 2020 07:30:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:05: 2000000 INFO @ Fri, 26 Jun 2020 07:30:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.05_summits.bed INFO @ Fri, 26 Jun 2020 07:30:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1197 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:30:09: 3000000 INFO @ Fri, 26 Jun 2020 07:30:14: 4000000 INFO @ Fri, 26 Jun 2020 07:30:18: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:30:18: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:30:18: #1 total tags in treatment: 4816975 INFO @ Fri, 26 Jun 2020 07:30:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:30:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:30:18: #1 tags after filtering in treatment: 4816975 INFO @ Fri, 26 Jun 2020 07:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:30:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:30:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:30:18: #2 number of paired peaks: 710 WARNING @ Fri, 26 Jun 2020 07:30:18: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Fri, 26 Jun 2020 07:30:18: start model_add_line... INFO @ Fri, 26 Jun 2020 07:30:18: start X-correlation... INFO @ Fri, 26 Jun 2020 07:30:18: end of X-cor INFO @ Fri, 26 Jun 2020 07:30:18: #2 finished! INFO @ Fri, 26 Jun 2020 07:30:18: #2 predicted fragment length is 155 bps INFO @ Fri, 26 Jun 2020 07:30:18: #2 alternative fragment length(s) may be 138,155 bps INFO @ Fri, 26 Jun 2020 07:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.10_model.r INFO @ Fri, 26 Jun 2020 07:30:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:30:18: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.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 @ Fri, 26 Jun 2020 07:30:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:30:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:30:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:31: 1000000 INFO @ Fri, 26 Jun 2020 07:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.10_summits.bed INFO @ Fri, 26 Jun 2020 07:30:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (572 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:30:36: 2000000 INFO @ Fri, 26 Jun 2020 07:30:41: 3000000 INFO @ Fri, 26 Jun 2020 07:30:47: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:30:51: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:30:51: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:30:51: #1 total tags in treatment: 4816975 INFO @ Fri, 26 Jun 2020 07:30:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:30:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:30:51: #1 tags after filtering in treatment: 4816975 INFO @ Fri, 26 Jun 2020 07:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:30:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:30:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:30:52: #2 number of paired peaks: 710 WARNING @ Fri, 26 Jun 2020 07:30:52: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Fri, 26 Jun 2020 07:30:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:30:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:30:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:30:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:30:52: #2 predicted fragment length is 155 bps INFO @ Fri, 26 Jun 2020 07:30:52: #2 alternative fragment length(s) may be 138,155 bps INFO @ Fri, 26 Jun 2020 07:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.20_model.r INFO @ Fri, 26 Jun 2020 07:30:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:30:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:31:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495011/SRX495011.20_summits.bed INFO @ Fri, 26 Jun 2020 07:31:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling