Job ID = 10166017 SRX = SRX8832102 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: 00:03:34 18464781 reads; of these: 18464781 (100.00%) were unpaired; of these: 2399684 (13.00%) aligned 0 times 13535377 (73.30%) aligned exactly 1 time 2529720 (13.70%) aligned >1 times 87.00% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 7974720 / 16065097 = 0.4964 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 20:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.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 20:32:05: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:32:05: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:32:10: 1000000 INFO @ Thu, 08 Oct 2020 20:32:15: 2000000 INFO @ Thu, 08 Oct 2020 20:32:20: 3000000 INFO @ Thu, 08 Oct 2020 20:32:26: 4000000 INFO @ Thu, 08 Oct 2020 20:32:31: 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 20:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.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 20:32:35: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:32:35: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:32:36: 6000000 INFO @ Thu, 08 Oct 2020 20:32:41: 1000000 INFO @ Thu, 08 Oct 2020 20:32:42: 7000000 INFO @ Thu, 08 Oct 2020 20:32:48: 2000000 INFO @ Thu, 08 Oct 2020 20:32:48: 8000000 INFO @ Thu, 08 Oct 2020 20:32:49: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:32:49: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:32:49: #1 total tags in treatment: 8090377 INFO @ Thu, 08 Oct 2020 20:32:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:32:49: #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 20:32:49: #1 tags after filtering in treatment: 8090377 INFO @ Thu, 08 Oct 2020 20:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:32:49: #1 finished! INFO @ Thu, 08 Oct 2020 20:32:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:32:50: #2 number of paired peaks: 5495 INFO @ Thu, 08 Oct 2020 20:32:50: start model_add_line... INFO @ Thu, 08 Oct 2020 20:32:50: start X-correlation... INFO @ Thu, 08 Oct 2020 20:32:50: end of X-cor INFO @ Thu, 08 Oct 2020 20:32:50: #2 finished! INFO @ Thu, 08 Oct 2020 20:32:50: #2 predicted fragment length is 164 bps INFO @ Thu, 08 Oct 2020 20:32:50: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 08 Oct 2020 20:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.05_model.r INFO @ Thu, 08 Oct 2020 20:32:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:32:54: 3000000 INFO @ Thu, 08 Oct 2020 20:33:00: 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 20:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.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 20:33:05: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:33:05: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:33:05: 5000000 INFO @ Thu, 08 Oct 2020 20:33:11: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:33:12: 1000000 INFO @ Thu, 08 Oct 2020 20:33:12: 6000000 INFO @ Thu, 08 Oct 2020 20:33:18: 7000000 INFO @ Thu, 08 Oct 2020 20:33:19: 2000000 INFO @ Thu, 08 Oct 2020 20:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.05_summits.bed INFO @ Thu, 08 Oct 2020 20:33:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8692 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:33:25: 8000000 INFO @ Thu, 08 Oct 2020 20:33:25: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:33:25: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:33:25: #1 total tags in treatment: 8090377 INFO @ Thu, 08 Oct 2020 20:33:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:33:25: #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 20:33:26: #1 tags after filtering in treatment: 8090377 INFO @ Thu, 08 Oct 2020 20:33:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:33:26: #1 finished! INFO @ Thu, 08 Oct 2020 20:33:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:33:26: 3000000 INFO @ Thu, 08 Oct 2020 20:33:26: #2 number of paired peaks: 5495 INFO @ Thu, 08 Oct 2020 20:33:26: start model_add_line... INFO @ Thu, 08 Oct 2020 20:33:27: start X-correlation... INFO @ Thu, 08 Oct 2020 20:33:27: end of X-cor INFO @ Thu, 08 Oct 2020 20:33:27: #2 finished! INFO @ Thu, 08 Oct 2020 20:33:27: #2 predicted fragment length is 164 bps INFO @ Thu, 08 Oct 2020 20:33:27: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 08 Oct 2020 20:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.10_model.r INFO @ Thu, 08 Oct 2020 20:33:27: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:33:33: 4000000 INFO @ Thu, 08 Oct 2020 20:33:39: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:33:46: 6000000 INFO @ Thu, 08 Oct 2020 20:33:47: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:33:52: 7000000 INFO @ Thu, 08 Oct 2020 20:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.10_summits.bed INFO @ Thu, 08 Oct 2020 20:33:57: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7091 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:33:59: 8000000 INFO @ Thu, 08 Oct 2020 20:33:59: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:33:59: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:33:59: #1 total tags in treatment: 8090377 INFO @ Thu, 08 Oct 2020 20:33:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:33:59: #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 20:33:59: #1 tags after filtering in treatment: 8090377 INFO @ Thu, 08 Oct 2020 20:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:33:59: #1 finished! INFO @ Thu, 08 Oct 2020 20:33:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:34:00: #2 number of paired peaks: 5495 INFO @ Thu, 08 Oct 2020 20:34:00: start model_add_line... INFO @ Thu, 08 Oct 2020 20:34:00: start X-correlation... INFO @ Thu, 08 Oct 2020 20:34:00: end of X-cor INFO @ Thu, 08 Oct 2020 20:34:00: #2 finished! INFO @ Thu, 08 Oct 2020 20:34:00: #2 predicted fragment length is 164 bps INFO @ Thu, 08 Oct 2020 20:34:00: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 08 Oct 2020 20:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.20_model.r INFO @ Thu, 08 Oct 2020 20:34:00: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:34:22: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832102/SRX8832102.20_summits.bed INFO @ Thu, 08 Oct 2020 20:34:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5527 records, 4 fields): 6 millis CompletedMACS2peakCalling