Job ID = 10166016 SRX = SRX8832106 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: 00:02:42 13247927 reads; of these: 13247927 (100.00%) were unpaired; of these: 1835941 (13.86%) aligned 0 times 9332389 (70.44%) aligned exactly 1 time 2079597 (15.70%) aligned >1 times 86.14% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 3034531 / 11411986 = 0.2659 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 20:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.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 20:30:11: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:30:11: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:30:17: 1000000 INFO @ Thu, 08 Oct 2020 20:30:22: 2000000 INFO @ Thu, 08 Oct 2020 20:30:27: 3000000 INFO @ Thu, 08 Oct 2020 20:30:32: 4000000 INFO @ Thu, 08 Oct 2020 20:30:37: 5000000 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 20:30:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.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 20:30:42: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:30:42: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:30:42: 6000000 INFO @ Thu, 08 Oct 2020 20:30:47: 1000000 INFO @ Thu, 08 Oct 2020 20:30:47: 7000000 INFO @ Thu, 08 Oct 2020 20:30:53: 2000000 INFO @ Thu, 08 Oct 2020 20:30:53: 8000000 INFO @ Thu, 08 Oct 2020 20:30:55: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:30:55: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:30:55: #1 total tags in treatment: 8377455 INFO @ Thu, 08 Oct 2020 20:30:55: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:30:55: #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 20:30:55: #1 tags after filtering in treatment: 8377455 INFO @ Thu, 08 Oct 2020 20:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:30:55: #1 finished! INFO @ Thu, 08 Oct 2020 20:30:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:30:56: #2 number of paired peaks: 1740 INFO @ Thu, 08 Oct 2020 20:30:56: start model_add_line... INFO @ Thu, 08 Oct 2020 20:30:56: start X-correlation... INFO @ Thu, 08 Oct 2020 20:30:56: end of X-cor INFO @ Thu, 08 Oct 2020 20:30:56: #2 finished! INFO @ Thu, 08 Oct 2020 20:30:56: #2 predicted fragment length is 149 bps INFO @ Thu, 08 Oct 2020 20:30:56: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 08 Oct 2020 20:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.05_model.r INFO @ Thu, 08 Oct 2020 20:30:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:30:58: 3000000 INFO @ Thu, 08 Oct 2020 20:31:04: 4000000 INFO @ Thu, 08 Oct 2020 20:31:09: 5000000 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 20:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.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 20:31:12: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:31:12: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:31:14: 6000000 INFO @ Thu, 08 Oct 2020 20:31:15: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:31:17: 1000000 INFO @ Thu, 08 Oct 2020 20:31:20: 7000000 INFO @ Thu, 08 Oct 2020 20:31:23: 2000000 INFO @ Thu, 08 Oct 2020 20:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.05_summits.bed INFO @ Thu, 08 Oct 2020 20:31:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6689 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:31:25: 8000000 INFO @ Thu, 08 Oct 2020 20:31:28: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:31:28: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:31:28: #1 total tags in treatment: 8377455 INFO @ Thu, 08 Oct 2020 20:31:28: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:31:28: #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 20:31:28: #1 tags after filtering in treatment: 8377455 INFO @ Thu, 08 Oct 2020 20:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:31:28: #1 finished! INFO @ Thu, 08 Oct 2020 20:31:28: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:31:28: #2 number of paired peaks: 1740 INFO @ Thu, 08 Oct 2020 20:31:28: start model_add_line... INFO @ Thu, 08 Oct 2020 20:31:28: start X-correlation... INFO @ Thu, 08 Oct 2020 20:31:28: end of X-cor INFO @ Thu, 08 Oct 2020 20:31:28: #2 finished! INFO @ Thu, 08 Oct 2020 20:31:28: 3000000 INFO @ Thu, 08 Oct 2020 20:31:28: #2 predicted fragment length is 149 bps INFO @ Thu, 08 Oct 2020 20:31:28: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 08 Oct 2020 20:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.10_model.r INFO @ Thu, 08 Oct 2020 20:31:29: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:31:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:31:34: 4000000 INFO @ Thu, 08 Oct 2020 20:31:39: 5000000 INFO @ Thu, 08 Oct 2020 20:31:44: 6000000 INFO @ Thu, 08 Oct 2020 20:31:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:31:50: 7000000 INFO @ Thu, 08 Oct 2020 20:31:55: 8000000 INFO @ Thu, 08 Oct 2020 20:31:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:31:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:31:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.10_summits.bed INFO @ Thu, 08 Oct 2020 20:31:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5086 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:31:57: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:31:57: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:31:57: #1 total tags in treatment: 8377455 INFO @ Thu, 08 Oct 2020 20:31:57: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:31:57: #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 20:31:57: #1 tags after filtering in treatment: 8377455 INFO @ Thu, 08 Oct 2020 20:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:31:57: #1 finished! INFO @ Thu, 08 Oct 2020 20:31:57: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:31:58: #2 number of paired peaks: 1740 INFO @ Thu, 08 Oct 2020 20:31:58: start model_add_line... INFO @ Thu, 08 Oct 2020 20:31:58: start X-correlation... INFO @ Thu, 08 Oct 2020 20:31:58: end of X-cor INFO @ Thu, 08 Oct 2020 20:31:58: #2 finished! INFO @ Thu, 08 Oct 2020 20:31:58: #2 predicted fragment length is 149 bps INFO @ Thu, 08 Oct 2020 20:31:58: #2 alternative fragment length(s) may be 149 bps INFO @ Thu, 08 Oct 2020 20:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.20_model.r INFO @ Thu, 08 Oct 2020 20:31:58: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:31:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:32:17: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832106/SRX8832106.20_summits.bed INFO @ Thu, 08 Oct 2020 20:32:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3505 records, 4 fields): 5 millis CompletedMACS2peakCalling