Job ID = 14160381 SRX = SRX8832086 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:13 11817326 reads; of these: 11817326 (100.00%) were unpaired; of these: 2544478 (21.53%) aligned 0 times 7891466 (66.78%) aligned exactly 1 time 1381382 (11.69%) aligned >1 times 78.47% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 5475455 / 9272848 = 0.5905 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 02:04:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.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 02:04:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:04:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:04:17: 1000000 INFO @ Thu, 09 Dec 2021 02:04:23: 2000000 INFO @ Thu, 09 Dec 2021 02:04:29: 3000000 INFO @ Thu, 09 Dec 2021 02:04:34: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:04:34: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:04:34: #1 total tags in treatment: 3797393 INFO @ Thu, 09 Dec 2021 02:04:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:04:34: #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 02:04:34: #1 tags after filtering in treatment: 3797393 INFO @ Thu, 09 Dec 2021 02:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:04:34: #1 finished! INFO @ Thu, 09 Dec 2021 02:04:34: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:04:35: #2 number of paired peaks: 4205 INFO @ Thu, 09 Dec 2021 02:04:35: start model_add_line... INFO @ Thu, 09 Dec 2021 02:04:35: start X-correlation... INFO @ Thu, 09 Dec 2021 02:04:35: end of X-cor INFO @ Thu, 09 Dec 2021 02:04:35: #2 finished! INFO @ Thu, 09 Dec 2021 02:04:35: #2 predicted fragment length is 168 bps INFO @ Thu, 09 Dec 2021 02:04:35: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 09 Dec 2021 02:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.05_model.r INFO @ Thu, 09 Dec 2021 02:04:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:04:35: #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 02:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.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 02:04:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:04:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:04:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:04:47: 1000000 INFO @ Thu, 09 Dec 2021 02:04:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:04:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:04:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.05_summits.bed INFO @ Thu, 09 Dec 2021 02:04:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5961 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:04:53: 2000000 INFO @ Thu, 09 Dec 2021 02:04:59: 3000000 INFO @ Thu, 09 Dec 2021 02:05:04: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:05:04: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:05:04: #1 total tags in treatment: 3797393 INFO @ Thu, 09 Dec 2021 02:05:04: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:05:04: #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 02:05:04: #1 tags after filtering in treatment: 3797393 INFO @ Thu, 09 Dec 2021 02:05:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:05:04: #1 finished! INFO @ Thu, 09 Dec 2021 02:05:04: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:05:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:05:05: #2 number of paired peaks: 4205 INFO @ Thu, 09 Dec 2021 02:05:05: start model_add_line... INFO @ Thu, 09 Dec 2021 02:05:05: start X-correlation... INFO @ Thu, 09 Dec 2021 02:05:05: end of X-cor INFO @ Thu, 09 Dec 2021 02:05:05: #2 finished! INFO @ Thu, 09 Dec 2021 02:05:05: #2 predicted fragment length is 168 bps INFO @ Thu, 09 Dec 2021 02:05:05: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 09 Dec 2021 02:05:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.10_model.r INFO @ Thu, 09 Dec 2021 02:05:05: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:05:05: #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 02:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.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 02:05:11: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:05:11: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:05:17: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:05:17: 1000000 INFO @ Thu, 09 Dec 2021 02:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.10_summits.bed INFO @ Thu, 09 Dec 2021 02:05:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4856 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:05:22: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:05:27: 3000000 INFO @ Thu, 09 Dec 2021 02:05:32: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:05:32: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:05:32: #1 total tags in treatment: 3797393 INFO @ Thu, 09 Dec 2021 02:05:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:05:32: #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 02:05:32: #1 tags after filtering in treatment: 3797393 INFO @ Thu, 09 Dec 2021 02:05:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:05:32: #1 finished! INFO @ Thu, 09 Dec 2021 02:05:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:05:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:05:32: #2 number of paired peaks: 4205 INFO @ Thu, 09 Dec 2021 02:05:32: start model_add_line... INFO @ Thu, 09 Dec 2021 02:05:32: start X-correlation... INFO @ Thu, 09 Dec 2021 02:05:32: end of X-cor INFO @ Thu, 09 Dec 2021 02:05:32: #2 finished! INFO @ Thu, 09 Dec 2021 02:05:32: #2 predicted fragment length is 168 bps INFO @ Thu, 09 Dec 2021 02:05:32: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 09 Dec 2021 02:05:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.20_model.r INFO @ Thu, 09 Dec 2021 02:05:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:05:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:05:44: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832086/SRX8832086.20_summits.bed INFO @ Thu, 09 Dec 2021 02:05:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3701 records, 4 fields): 5 millis CompletedMACS2peakCalling