Job ID = 14160487 SRX = SRX9904335 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6721263 spots for SRR13491821/SRR13491821.sra Written 6721263 spots for SRR13491821/SRR13491821.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160612 ("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: 00:01:09 6721263 reads; of these: 6721263 (100.00%) were unpaired; of these: 2355994 (35.05%) aligned 0 times 3009075 (44.77%) aligned exactly 1 time 1356194 (20.18%) aligned >1 times 64.95% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 589705 / 4365269 = 0.1351 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:51:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.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, 09 Dec 2021 02:51:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:51:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:51:18: 1000000 INFO @ Thu, 09 Dec 2021 02:51:24: 2000000 INFO @ Thu, 09 Dec 2021 02:51:29: 3000000 INFO @ Thu, 09 Dec 2021 02:51:33: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:51:33: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:51:33: #1 total tags in treatment: 3775564 INFO @ Thu, 09 Dec 2021 02:51:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:51:33: #1 tags after filtering in treatment: 3775564 INFO @ Thu, 09 Dec 2021 02:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:51:33: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:33: #2 number of paired peaks: 2180 INFO @ Thu, 09 Dec 2021 02:51:33: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:33: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:33: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:33: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:33: #2 predicted fragment length is 174 bps INFO @ Thu, 09 Dec 2021 02:51:33: #2 alternative fragment length(s) may be 4,99,174 bps INFO @ Thu, 09 Dec 2021 02:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.05_model.r INFO @ Thu, 09 Dec 2021 02:51:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:33: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:51:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.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, 09 Dec 2021 02:51:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:51:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.05_summits.bed INFO @ Thu, 09 Dec 2021 02:51:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (972 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:51:48: 1000000 INFO @ Thu, 09 Dec 2021 02:51:54: 2000000 INFO @ Thu, 09 Dec 2021 02:51:59: 3000000 INFO @ Thu, 09 Dec 2021 02:52:03: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:52:03: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:52:03: #1 total tags in treatment: 3775564 INFO @ Thu, 09 Dec 2021 02:52:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:52:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:52:03: #1 tags after filtering in treatment: 3775564 INFO @ Thu, 09 Dec 2021 02:52:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:52:03: #1 finished! INFO @ Thu, 09 Dec 2021 02:52:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:52:03: #2 number of paired peaks: 2180 INFO @ Thu, 09 Dec 2021 02:52:03: start model_add_line... INFO @ Thu, 09 Dec 2021 02:52:03: start X-correlation... INFO @ Thu, 09 Dec 2021 02:52:03: end of X-cor INFO @ Thu, 09 Dec 2021 02:52:03: #2 finished! INFO @ Thu, 09 Dec 2021 02:52:03: #2 predicted fragment length is 174 bps INFO @ Thu, 09 Dec 2021 02:52:03: #2 alternative fragment length(s) may be 4,99,174 bps INFO @ Thu, 09 Dec 2021 02:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.10_model.r INFO @ Thu, 09 Dec 2021 02:52:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:52:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:52:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.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, 09 Dec 2021 02:52:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:52:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.10_summits.bed INFO @ Thu, 09 Dec 2021 02:52:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:52:18: 1000000 INFO @ Thu, 09 Dec 2021 02:52:24: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:52:29: 3000000 INFO @ Thu, 09 Dec 2021 02:52:33: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:52:33: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:52:33: #1 total tags in treatment: 3775564 INFO @ Thu, 09 Dec 2021 02:52:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:52:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:52:33: #1 tags after filtering in treatment: 3775564 INFO @ Thu, 09 Dec 2021 02:52:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:52:33: #1 finished! INFO @ Thu, 09 Dec 2021 02:52:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:52:33: #2 number of paired peaks: 2180 INFO @ Thu, 09 Dec 2021 02:52:33: start model_add_line... INFO @ Thu, 09 Dec 2021 02:52:33: start X-correlation... INFO @ Thu, 09 Dec 2021 02:52:33: end of X-cor INFO @ Thu, 09 Dec 2021 02:52:33: #2 finished! INFO @ Thu, 09 Dec 2021 02:52:33: #2 predicted fragment length is 174 bps INFO @ Thu, 09 Dec 2021 02:52:33: #2 alternative fragment length(s) may be 4,99,174 bps INFO @ Thu, 09 Dec 2021 02:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.20_model.r INFO @ Thu, 09 Dec 2021 02:52:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:52:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:52:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9904335/SRX9904335.20_summits.bed INFO @ Thu, 09 Dec 2021 02:52:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling