Job ID = 10165982 SRX = SRX8832096 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: 00:02:20 10882888 reads; of these: 10882888 (100.00%) were unpaired; of these: 936313 (8.60%) aligned 0 times 8292845 (76.20%) aligned exactly 1 time 1653730 (15.20%) aligned >1 times 91.40% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:21 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] 4515827 / 9946575 = 0.4540 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 20:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.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 20:26:36: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:26:36: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:26:41: 1000000 INFO @ Thu, 08 Oct 2020 20:26:46: 2000000 INFO @ Thu, 08 Oct 2020 20:26:51: 3000000 INFO @ Thu, 08 Oct 2020 20:26:58: 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 20:27:04: 5000000 INFO @ Thu, 08 Oct 2020 20:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.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 20:27:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:27:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:27:07: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:27:07: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:27:07: #1 total tags in treatment: 5430748 INFO @ Thu, 08 Oct 2020 20:27:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:07: #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 20:27:07: #1 tags after filtering in treatment: 5430748 INFO @ Thu, 08 Oct 2020 20:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:07: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:08: #2 number of paired peaks: 3736 INFO @ Thu, 08 Oct 2020 20:27:08: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:08: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:08: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:08: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:08: #2 predicted fragment length is 145 bps INFO @ Thu, 08 Oct 2020 20:27:08: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 08 Oct 2020 20:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.05_model.r INFO @ Thu, 08 Oct 2020 20:27:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:27:13: 1000000 INFO @ Thu, 08 Oct 2020 20:27:18: 2000000 INFO @ Thu, 08 Oct 2020 20:27:23: 3000000 INFO @ Thu, 08 Oct 2020 20:27:23: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:28: 4000000 INFO @ Thu, 08 Oct 2020 20:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.05_summits.bed INFO @ Thu, 08 Oct 2020 20:27:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6267 records, 4 fields): 10 millis CompletedMACS2peakCalling 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 20:27:33: 5000000 INFO @ Thu, 08 Oct 2020 20:27:35: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:27:35: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:27:35: #1 total tags in treatment: 5430748 INFO @ Thu, 08 Oct 2020 20:27:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:35: #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 20:27:35: #1 tags after filtering in treatment: 5430748 INFO @ Thu, 08 Oct 2020 20:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:36: #2 number of paired peaks: 3736 INFO @ Thu, 08 Oct 2020 20:27:36: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:36: #2 predicted fragment length is 145 bps INFO @ Thu, 08 Oct 2020 20:27:36: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 08 Oct 2020 20:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.10_model.r INFO @ Thu, 08 Oct 2020 20:27:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.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 20:27:36: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:27:36: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:27:41: 1000000 INFO @ Thu, 08 Oct 2020 20:27:46: 2000000 INFO @ Thu, 08 Oct 2020 20:27:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:51: 3000000 INFO @ Thu, 08 Oct 2020 20:27:56: 4000000 INFO @ Thu, 08 Oct 2020 20:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.10_summits.bed INFO @ Thu, 08 Oct 2020 20:27:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5208 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:28:01: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:28:03: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:28:03: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:28:03: #1 total tags in treatment: 5430748 INFO @ Thu, 08 Oct 2020 20:28:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:03: #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 20:28:03: #1 tags after filtering in treatment: 5430748 INFO @ Thu, 08 Oct 2020 20:28:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:03: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:04: #2 number of paired peaks: 3736 INFO @ Thu, 08 Oct 2020 20:28:04: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:04: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:04: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:04: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:04: #2 predicted fragment length is 145 bps INFO @ Thu, 08 Oct 2020 20:28:04: #2 alternative fragment length(s) may be 145 bps INFO @ Thu, 08 Oct 2020 20:28:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.20_model.r INFO @ Thu, 08 Oct 2020 20:28:04: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:28:18: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832096/SRX8832096.20_summits.bed INFO @ Thu, 08 Oct 2020 20:28:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4060 records, 4 fields): 6 millis CompletedMACS2peakCalling