Job ID = 14160601 SRX = SRX9904333 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: 00:02:02 7843902 reads; of these: 7843902 (100.00%) were unpaired; of these: 489521 (6.24%) aligned 0 times 6449886 (82.23%) aligned exactly 1 time 904495 (11.53%) aligned >1 times 93.76% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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] 1022451 / 7354381 = 0.1390 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 03:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.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 03:27:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:27:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:27:47: 1000000 INFO @ Thu, 09 Dec 2021 03:27:55: 2000000 INFO @ Thu, 09 Dec 2021 03:28:03: 3000000 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 03:28:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.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 03:28:08: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:28:08: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:11: 4000000 INFO @ Thu, 09 Dec 2021 03:28:16: 1000000 INFO @ Thu, 09 Dec 2021 03:28:18: 5000000 INFO @ Thu, 09 Dec 2021 03:28:23: 2000000 INFO @ Thu, 09 Dec 2021 03:28:26: 6000000 INFO @ Thu, 09 Dec 2021 03:28:29: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:28:29: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:28:29: #1 total tags in treatment: 6331930 INFO @ Thu, 09 Dec 2021 03:28:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:29: #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 03:28:29: #1 tags after filtering in treatment: 6331930 INFO @ Thu, 09 Dec 2021 03:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:28:29: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:30: #2 number of paired peaks: 2340 INFO @ Thu, 09 Dec 2021 03:28:30: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:30: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:30: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:30: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:30: #2 predicted fragment length is 323 bps INFO @ Thu, 09 Dec 2021 03:28:30: #2 alternative fragment length(s) may be 323 bps INFO @ Thu, 09 Dec 2021 03:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.05_model.r INFO @ Thu, 09 Dec 2021 03:28:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:31: 3000000 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 03:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.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 03:28:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:28:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:38: 4000000 INFO @ Thu, 09 Dec 2021 03:28:46: 1000000 INFO @ Thu, 09 Dec 2021 03:28:46: 5000000 INFO @ Thu, 09 Dec 2021 03:28:54: 6000000 INFO @ Thu, 09 Dec 2021 03:28:54: 2000000 INFO @ Thu, 09 Dec 2021 03:28:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:28:56: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:28:56: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:28:56: #1 total tags in treatment: 6331930 INFO @ Thu, 09 Dec 2021 03:28:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:56: #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 03:28:56: #1 tags after filtering in treatment: 6331930 INFO @ Thu, 09 Dec 2021 03:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:28:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:57: #2 number of paired peaks: 2340 INFO @ Thu, 09 Dec 2021 03:28:57: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:57: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:57: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:57: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:57: #2 predicted fragment length is 323 bps INFO @ Thu, 09 Dec 2021 03:28:57: #2 alternative fragment length(s) may be 323 bps INFO @ Thu, 09 Dec 2021 03:28:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.10_model.r INFO @ Thu, 09 Dec 2021 03:28:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:02: 3000000 INFO @ Thu, 09 Dec 2021 03:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.05_summits.bed INFO @ Thu, 09 Dec 2021 03:29:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3286 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:09: 4000000 INFO @ Thu, 09 Dec 2021 03:29:16: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:29:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:24: 6000000 INFO @ Thu, 09 Dec 2021 03:29:26: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:29:26: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:29:26: #1 total tags in treatment: 6331930 INFO @ Thu, 09 Dec 2021 03:29:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:26: #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 03:29:27: #1 tags after filtering in treatment: 6331930 INFO @ Thu, 09 Dec 2021 03:29:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:29:27: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:27: #2 number of paired peaks: 2340 INFO @ Thu, 09 Dec 2021 03:29:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:27: #2 predicted fragment length is 323 bps INFO @ Thu, 09 Dec 2021 03:29:27: #2 alternative fragment length(s) may be 323 bps INFO @ Thu, 09 Dec 2021 03:29:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.20_model.r INFO @ Thu, 09 Dec 2021 03:29:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.10_summits.bed INFO @ Thu, 09 Dec 2021 03:29:34: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1951 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:29:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904333/SRX9904333.20_summits.bed INFO @ Thu, 09 Dec 2021 03:30:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (863 records, 4 fields): 5 millis CompletedMACS2peakCalling