Job ID = 6367619 SRX = SRX341787 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:37:44 prefetch.2.10.7: 1) Downloading 'SRR959928'... 2020-06-15T23:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:58 prefetch.2.10.7: 1) 'SRR959928' was downloaded successfully Read 17389010 spots for SRR959928/SRR959928.sra Written 17389010 spots for SRR959928/SRR959928.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: 00:05:04 17389010 reads; of these: 17389010 (100.00%) were unpaired; of these: 3026980 (17.41%) aligned 0 times 12344858 (70.99%) aligned exactly 1 time 2017172 (11.60%) aligned >1 times 82.59% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 6041587 / 14362030 = 0.4207 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 08:51:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.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 08:51:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:02: 1000000 INFO @ Tue, 16 Jun 2020 08:52:10: 2000000 INFO @ Tue, 16 Jun 2020 08:52:18: 3000000 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 08:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.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 08:52:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:26: 4000000 INFO @ Tue, 16 Jun 2020 08:52:32: 1000000 INFO @ Tue, 16 Jun 2020 08:52:34: 5000000 INFO @ Tue, 16 Jun 2020 08:52:40: 2000000 INFO @ Tue, 16 Jun 2020 08:52:41: 6000000 INFO @ Tue, 16 Jun 2020 08:52:48: 3000000 INFO @ Tue, 16 Jun 2020 08:52:49: 7000000 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 08:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.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 08:52:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:56: 4000000 INFO @ Tue, 16 Jun 2020 08:52:57: 8000000 INFO @ Tue, 16 Jun 2020 08:52:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:52:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:52:59: #1 total tags in treatment: 8320443 INFO @ Tue, 16 Jun 2020 08:52:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:59: #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 08:53:00: #1 tags after filtering in treatment: 8320443 INFO @ Tue, 16 Jun 2020 08:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:00: #2 number of paired peaks: 315 WARNING @ Tue, 16 Jun 2020 08:53:00: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:00: #2 predicted fragment length is 111 bps INFO @ Tue, 16 Jun 2020 08:53:00: #2 alternative fragment length(s) may be 4,111,138 bps INFO @ Tue, 16 Jun 2020 08:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.05_model.r INFO @ Tue, 16 Jun 2020 08:53:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:02: 1000000 INFO @ Tue, 16 Jun 2020 08:53:04: 5000000 INFO @ Tue, 16 Jun 2020 08:53:10: 2000000 INFO @ Tue, 16 Jun 2020 08:53:11: 6000000 INFO @ Tue, 16 Jun 2020 08:53:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:18: 3000000 INFO @ Tue, 16 Jun 2020 08:53:19: 7000000 INFO @ Tue, 16 Jun 2020 08:53:26: 4000000 INFO @ Tue, 16 Jun 2020 08:53:27: 8000000 INFO @ Tue, 16 Jun 2020 08:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.05_summits.bed INFO @ Tue, 16 Jun 2020 08:53:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:53:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:53:30: #1 total tags in treatment: 8320443 INFO @ Tue, 16 Jun 2020 08:53:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:30: #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 08:53:30: #1 tags after filtering in treatment: 8320443 INFO @ Tue, 16 Jun 2020 08:53:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:31: #2 number of paired peaks: 315 WARNING @ Tue, 16 Jun 2020 08:53:31: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:31: #2 predicted fragment length is 111 bps INFO @ Tue, 16 Jun 2020 08:53:31: #2 alternative fragment length(s) may be 4,111,138 bps INFO @ Tue, 16 Jun 2020 08:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.10_model.r INFO @ Tue, 16 Jun 2020 08:53:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:34: 5000000 INFO @ Tue, 16 Jun 2020 08:53:41: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:53:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:53:49: 7000000 INFO @ Tue, 16 Jun 2020 08:53:57: 8000000 INFO @ Tue, 16 Jun 2020 08:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.10_summits.bed INFO @ Tue, 16 Jun 2020 08:53:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:53:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:53:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:53:59: #1 total tags in treatment: 8320443 INFO @ Tue, 16 Jun 2020 08:53:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:59: #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 08:53:59: #1 tags after filtering in treatment: 8320443 INFO @ Tue, 16 Jun 2020 08:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:53:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:00: #2 number of paired peaks: 315 WARNING @ Tue, 16 Jun 2020 08:54:00: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:00: #2 predicted fragment length is 111 bps INFO @ Tue, 16 Jun 2020 08:54:00: #2 alternative fragment length(s) may be 4,111,138 bps INFO @ Tue, 16 Jun 2020 08:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.20_model.r INFO @ Tue, 16 Jun 2020 08:54:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:54:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341787/SRX341787.20_summits.bed INFO @ Tue, 16 Jun 2020 08:54:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (97 records, 4 fields): 2 millis CompletedMACS2peakCalling