Job ID = 10166036 SRX = SRX8832104 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: 00:03:51 18341985 reads; of these: 18341985 (100.00%) were unpaired; of these: 801996 (4.37%) aligned 0 times 14611765 (79.66%) aligned exactly 1 time 2928224 (15.96%) aligned >1 times 95.63% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 8220027 / 17539989 = 0.4686 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 20:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.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 20:34:11: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:34:11: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:34:16: 1000000 INFO @ Thu, 08 Oct 2020 20:34:21: 2000000 INFO @ Thu, 08 Oct 2020 20:34:27: 3000000 INFO @ Thu, 08 Oct 2020 20:34:32: 4000000 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 20:34:38: 5000000 INFO @ Thu, 08 Oct 2020 20:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.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 20:34:40: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:34:40: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:34:43: 6000000 INFO @ Thu, 08 Oct 2020 20:34:47: 1000000 INFO @ Thu, 08 Oct 2020 20:34:49: 7000000 INFO @ Thu, 08 Oct 2020 20:34:53: 2000000 INFO @ Thu, 08 Oct 2020 20:34:56: 8000000 INFO @ Thu, 08 Oct 2020 20:34:59: 3000000 INFO @ Thu, 08 Oct 2020 20:35:02: 9000000 INFO @ Thu, 08 Oct 2020 20:35:04: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:35:04: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:35:04: #1 total tags in treatment: 9319962 INFO @ Thu, 08 Oct 2020 20:35:04: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:35:04: #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 20:35:04: #1 tags after filtering in treatment: 9319962 INFO @ Thu, 08 Oct 2020 20:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:35:04: #1 finished! INFO @ Thu, 08 Oct 2020 20:35:04: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:35:05: #2 number of paired peaks: 3609 INFO @ Thu, 08 Oct 2020 20:35:05: start model_add_line... INFO @ Thu, 08 Oct 2020 20:35:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:35:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:35:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:35:05: #2 predicted fragment length is 157 bps INFO @ Thu, 08 Oct 2020 20:35:05: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 08 Oct 2020 20:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.05_model.r INFO @ Thu, 08 Oct 2020 20:35:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:35:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:35:05: 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 20:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.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 20:35:10: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:35:10: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:35:11: 5000000 INFO @ Thu, 08 Oct 2020 20:35:16: 1000000 INFO @ Thu, 08 Oct 2020 20:35:17: 6000000 INFO @ Thu, 08 Oct 2020 20:35:23: 2000000 INFO @ Thu, 08 Oct 2020 20:35:23: 7000000 INFO @ Thu, 08 Oct 2020 20:35:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:35:29: 3000000 INFO @ Thu, 08 Oct 2020 20:35:29: 8000000 INFO @ Thu, 08 Oct 2020 20:35:35: 4000000 INFO @ Thu, 08 Oct 2020 20:35:36: 9000000 INFO @ Thu, 08 Oct 2020 20:35:37: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:35:37: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:35:37: #1 total tags in treatment: 9319962 INFO @ Thu, 08 Oct 2020 20:35:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:35:37: #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 20:35:38: #1 tags after filtering in treatment: 9319962 INFO @ Thu, 08 Oct 2020 20:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:35:38: #1 finished! INFO @ Thu, 08 Oct 2020 20:35:38: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.05_summits.bed INFO @ Thu, 08 Oct 2020 20:35:38: Done! INFO @ Thu, 08 Oct 2020 20:35:38: #2 number of paired peaks: 3609 INFO @ Thu, 08 Oct 2020 20:35:38: start model_add_line... INFO @ Thu, 08 Oct 2020 20:35:39: start X-correlation... INFO @ Thu, 08 Oct 2020 20:35:39: end of X-cor INFO @ Thu, 08 Oct 2020 20:35:39: #2 finished! INFO @ Thu, 08 Oct 2020 20:35:39: #2 predicted fragment length is 157 bps INFO @ Thu, 08 Oct 2020 20:35:39: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 08 Oct 2020 20:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.10_model.r INFO @ Thu, 08 Oct 2020 20:35:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:35:41: 5000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6493 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:35:47: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:35:52: 7000000 INFO @ Thu, 08 Oct 2020 20:35:58: 8000000 INFO @ Thu, 08 Oct 2020 20:36:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:36:03: 9000000 INFO @ Thu, 08 Oct 2020 20:36:05: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:36:05: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:36:05: #1 total tags in treatment: 9319962 INFO @ Thu, 08 Oct 2020 20:36:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:36:05: #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 20:36:05: #1 tags after filtering in treatment: 9319962 INFO @ Thu, 08 Oct 2020 20:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:36:05: #1 finished! INFO @ Thu, 08 Oct 2020 20:36:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:36:05: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:36:06: #2 number of paired peaks: 3609 INFO @ Thu, 08 Oct 2020 20:36:06: start model_add_line... INFO @ Thu, 08 Oct 2020 20:36:06: start X-correlation... INFO @ Thu, 08 Oct 2020 20:36:06: end of X-cor INFO @ Thu, 08 Oct 2020 20:36:06: #2 finished! INFO @ Thu, 08 Oct 2020 20:36:06: #2 predicted fragment length is 157 bps INFO @ Thu, 08 Oct 2020 20:36:06: #2 alternative fragment length(s) may be 157 bps INFO @ Thu, 08 Oct 2020 20:36:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.20_model.r INFO @ Thu, 08 Oct 2020 20:36:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:36:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.10_summits.bed INFO @ Thu, 08 Oct 2020 20:36:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5357 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:36:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832104/SRX8832104.20_summits.bed INFO @ Thu, 08 Oct 2020 20:36:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4288 records, 4 fields): 6 millis CompletedMACS2peakCalling