Job ID = 10165736 SRX = SRX8832089 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19742564 spots for SRR12332047/SRR12332047.sra Written 19742564 spots for SRR12332047/SRR12332047.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165971 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:08 19742564 reads; of these: 19742564 (100.00%) were unpaired; of these: 923405 (4.68%) aligned 0 times 16341910 (82.78%) aligned exactly 1 time 2477249 (12.55%) aligned >1 times 95.32% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 9734036 / 18819159 = 0.5172 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 @ Thu, 08 Oct 2020 19:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.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 @ Thu, 08 Oct 2020 19:51:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:51:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:51:20: 1000000 INFO @ Thu, 08 Oct 2020 19:51:25: 2000000 INFO @ Thu, 08 Oct 2020 19:51:31: 3000000 INFO @ Thu, 08 Oct 2020 19:51:36: 4000000 INFO @ Thu, 08 Oct 2020 19:51:41: 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 @ Thu, 08 Oct 2020 19:51:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.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 @ Thu, 08 Oct 2020 19:51:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:51:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:51:47: 6000000 INFO @ Thu, 08 Oct 2020 19:51:51: 1000000 INFO @ Thu, 08 Oct 2020 19:51:53: 7000000 INFO @ Thu, 08 Oct 2020 19:51:57: 2000000 INFO @ Thu, 08 Oct 2020 19:51:59: 8000000 INFO @ Thu, 08 Oct 2020 19:52:02: 3000000 INFO @ Thu, 08 Oct 2020 19:52:04: 9000000 INFO @ Thu, 08 Oct 2020 19:52:05: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:52:05: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:52:05: #1 total tags in treatment: 9085123 INFO @ Thu, 08 Oct 2020 19:52:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:52:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:52:05: #1 tags after filtering in treatment: 9085123 INFO @ Thu, 08 Oct 2020 19:52:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:52:05: #1 finished! INFO @ Thu, 08 Oct 2020 19:52:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:52:06: #2 number of paired peaks: 3901 INFO @ Thu, 08 Oct 2020 19:52:06: start model_add_line... INFO @ Thu, 08 Oct 2020 19:52:06: start X-correlation... INFO @ Thu, 08 Oct 2020 19:52:06: end of X-cor INFO @ Thu, 08 Oct 2020 19:52:06: #2 finished! INFO @ Thu, 08 Oct 2020 19:52:06: #2 predicted fragment length is 142 bps INFO @ Thu, 08 Oct 2020 19:52:06: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 08 Oct 2020 19:52:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.05_model.r INFO @ Thu, 08 Oct 2020 19:52:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:52:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:52:08: 4000000 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 @ Thu, 08 Oct 2020 19:52:13: 5000000 INFO @ Thu, 08 Oct 2020 19:52:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.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 @ Thu, 08 Oct 2020 19:52:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:52:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:52:19: 6000000 INFO @ Thu, 08 Oct 2020 19:52:21: 1000000 INFO @ Thu, 08 Oct 2020 19:52:25: 7000000 INFO @ Thu, 08 Oct 2020 19:52:27: 2000000 INFO @ Thu, 08 Oct 2020 19:52:27: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:52:31: 8000000 INFO @ Thu, 08 Oct 2020 19:52:32: 3000000 INFO @ Thu, 08 Oct 2020 19:52:37: 9000000 INFO @ Thu, 08 Oct 2020 19:52:37: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:52:37: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:52:37: #1 total tags in treatment: 9085123 INFO @ Thu, 08 Oct 2020 19:52:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:52:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:52:37: #1 tags after filtering in treatment: 9085123 INFO @ Thu, 08 Oct 2020 19:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:52:37: #1 finished! INFO @ Thu, 08 Oct 2020 19:52:37: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.05_summits.bed INFO @ Thu, 08 Oct 2020 19:52:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7678 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:38: 4000000 INFO @ Thu, 08 Oct 2020 19:52:38: #2 number of paired peaks: 3901 INFO @ Thu, 08 Oct 2020 19:52:38: start model_add_line... INFO @ Thu, 08 Oct 2020 19:52:38: start X-correlation... INFO @ Thu, 08 Oct 2020 19:52:38: end of X-cor INFO @ Thu, 08 Oct 2020 19:52:38: #2 finished! INFO @ Thu, 08 Oct 2020 19:52:38: #2 predicted fragment length is 142 bps INFO @ Thu, 08 Oct 2020 19:52:38: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 08 Oct 2020 19:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.10_model.r INFO @ Thu, 08 Oct 2020 19:52:38: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:52:44: 5000000 INFO @ Thu, 08 Oct 2020 19:52:49: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:52:55: 7000000 INFO @ Thu, 08 Oct 2020 19:52:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:53:00: 8000000 INFO @ Thu, 08 Oct 2020 19:53:06: 9000000 INFO @ Thu, 08 Oct 2020 19:53:06: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:53:06: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:53:06: #1 total tags in treatment: 9085123 INFO @ Thu, 08 Oct 2020 19:53:06: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:53:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:53:07: #1 tags after filtering in treatment: 9085123 INFO @ Thu, 08 Oct 2020 19:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:53:07: #1 finished! INFO @ Thu, 08 Oct 2020 19:53:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:53:07: #2 number of paired peaks: 3901 INFO @ Thu, 08 Oct 2020 19:53:07: start model_add_line... INFO @ Thu, 08 Oct 2020 19:53:08: start X-correlation... INFO @ Thu, 08 Oct 2020 19:53:08: end of X-cor INFO @ Thu, 08 Oct 2020 19:53:08: #2 finished! INFO @ Thu, 08 Oct 2020 19:53:08: #2 predicted fragment length is 142 bps INFO @ Thu, 08 Oct 2020 19:53:08: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 08 Oct 2020 19:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.20_model.r INFO @ Thu, 08 Oct 2020 19:53:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.10_summits.bed INFO @ Thu, 08 Oct 2020 19:53:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6485 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:53:30: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832089/SRX8832089.20_summits.bed INFO @ Thu, 08 Oct 2020 19:53:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5175 records, 4 fields): 7 millis CompletedMACS2peakCalling