Job ID = 10165881 SRX = SRX8832065 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: 00:04:17 20163291 reads; of these: 20163291 (100.00%) were unpaired; of these: 302883 (1.50%) aligned 0 times 16862707 (83.63%) aligned exactly 1 time 2997701 (14.87%) aligned >1 times 98.50% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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 12 files... [bam_rmdupse_core] 3144791 / 19860408 = 0.1583 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 20:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.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 20:15:30: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:15:30: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:15:35: 1000000 INFO @ Thu, 08 Oct 2020 20:15:41: 2000000 INFO @ Thu, 08 Oct 2020 20:15:46: 3000000 INFO @ Thu, 08 Oct 2020 20:15:51: 4000000 INFO @ Thu, 08 Oct 2020 20:15:57: 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 20:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.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 20:16:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:16:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:16:02: 6000000 INFO @ Thu, 08 Oct 2020 20:16:08: 1000000 INFO @ Thu, 08 Oct 2020 20:16:09: 7000000 INFO @ Thu, 08 Oct 2020 20:16:15: 8000000 INFO @ Thu, 08 Oct 2020 20:16:15: 2000000 INFO @ Thu, 08 Oct 2020 20:16:21: 9000000 INFO @ Thu, 08 Oct 2020 20:16:22: 3000000 INFO @ Thu, 08 Oct 2020 20:16:28: 10000000 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 20:16:29: 4000000 INFO @ Thu, 08 Oct 2020 20:16:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.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 20:16:30: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:16:30: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:16:34: 11000000 INFO @ Thu, 08 Oct 2020 20:16:36: 5000000 INFO @ Thu, 08 Oct 2020 20:16:38: 1000000 INFO @ Thu, 08 Oct 2020 20:16:40: 12000000 INFO @ Thu, 08 Oct 2020 20:16:44: 6000000 INFO @ Thu, 08 Oct 2020 20:16:45: 2000000 INFO @ Thu, 08 Oct 2020 20:16:47: 13000000 INFO @ Thu, 08 Oct 2020 20:16:51: 7000000 INFO @ Thu, 08 Oct 2020 20:16:52: 3000000 INFO @ Thu, 08 Oct 2020 20:16:53: 14000000 INFO @ Thu, 08 Oct 2020 20:16:58: 8000000 INFO @ Thu, 08 Oct 2020 20:16:59: 4000000 INFO @ Thu, 08 Oct 2020 20:17:00: 15000000 INFO @ Thu, 08 Oct 2020 20:17:05: 9000000 INFO @ Thu, 08 Oct 2020 20:17:06: 16000000 INFO @ Thu, 08 Oct 2020 20:17:07: 5000000 INFO @ Thu, 08 Oct 2020 20:17:11: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:17:11: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:17:11: #1 total tags in treatment: 16715617 INFO @ Thu, 08 Oct 2020 20:17:11: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:17:11: #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 20:17:11: #1 tags after filtering in treatment: 16715617 INFO @ Thu, 08 Oct 2020 20:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:17:11: #1 finished! INFO @ Thu, 08 Oct 2020 20:17:11: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:17:12: 10000000 INFO @ Thu, 08 Oct 2020 20:17:12: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:17:12: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 20:17:12: start model_add_line... INFO @ Thu, 08 Oct 2020 20:17:12: start X-correlation... INFO @ Thu, 08 Oct 2020 20:17:12: end of X-cor INFO @ Thu, 08 Oct 2020 20:17:12: #2 finished! INFO @ Thu, 08 Oct 2020 20:17:12: #2 predicted fragment length is 122 bps INFO @ Thu, 08 Oct 2020 20:17:12: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 08 Oct 2020 20:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_model.r INFO @ Thu, 08 Oct 2020 20:17:12: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:17:14: 6000000 INFO @ Thu, 08 Oct 2020 20:17:19: 11000000 INFO @ Thu, 08 Oct 2020 20:17:21: 7000000 INFO @ Thu, 08 Oct 2020 20:17:26: 12000000 INFO @ Thu, 08 Oct 2020 20:17:28: 8000000 INFO @ Thu, 08 Oct 2020 20:17:33: 13000000 INFO @ Thu, 08 Oct 2020 20:17:35: 9000000 INFO @ Thu, 08 Oct 2020 20:17:40: 14000000 INFO @ Thu, 08 Oct 2020 20:17:42: 10000000 INFO @ Thu, 08 Oct 2020 20:17:46: 15000000 INFO @ Thu, 08 Oct 2020 20:17:47: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:17:49: 11000000 INFO @ Thu, 08 Oct 2020 20:17:53: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:17:56: 12000000 INFO @ Thu, 08 Oct 2020 20:17:58: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:17:58: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:17:58: #1 total tags in treatment: 16715617 INFO @ Thu, 08 Oct 2020 20:17:58: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:17:58: #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 20:17:58: #1 tags after filtering in treatment: 16715617 INFO @ Thu, 08 Oct 2020 20:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:17:58: #1 finished! INFO @ Thu, 08 Oct 2020 20:17:58: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:18:00: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:18:00: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 20:18:00: start model_add_line... INFO @ Thu, 08 Oct 2020 20:18:00: start X-correlation... INFO @ Thu, 08 Oct 2020 20:18:00: end of X-cor INFO @ Thu, 08 Oct 2020 20:18:00: #2 finished! INFO @ Thu, 08 Oct 2020 20:18:00: #2 predicted fragment length is 122 bps INFO @ Thu, 08 Oct 2020 20:18:00: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 08 Oct 2020 20:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_model.r INFO @ Thu, 08 Oct 2020 20:18:00: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:18:02: 13000000 INFO @ Thu, 08 Oct 2020 20:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_summits.bed INFO @ Thu, 08 Oct 2020 20:18:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7499 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:18:09: 14000000 INFO @ Thu, 08 Oct 2020 20:18:15: 15000000 INFO @ Thu, 08 Oct 2020 20:18:22: 16000000 INFO @ Thu, 08 Oct 2020 20:18:26: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:18:26: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:18:26: #1 total tags in treatment: 16715617 INFO @ Thu, 08 Oct 2020 20:18:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:18:26: #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 20:18:27: #1 tags after filtering in treatment: 16715617 INFO @ Thu, 08 Oct 2020 20:18:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:18:27: #1 finished! INFO @ Thu, 08 Oct 2020 20:18:27: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:18:28: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:18:28: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 20:18:28: start model_add_line... INFO @ Thu, 08 Oct 2020 20:18:28: start X-correlation... INFO @ Thu, 08 Oct 2020 20:18:28: end of X-cor INFO @ Thu, 08 Oct 2020 20:18:28: #2 finished! INFO @ Thu, 08 Oct 2020 20:18:28: #2 predicted fragment length is 122 bps INFO @ Thu, 08 Oct 2020 20:18:28: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 08 Oct 2020 20:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_model.r INFO @ Thu, 08 Oct 2020 20:18:28: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:18:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:18:32: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:18:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_summits.bed INFO @ Thu, 08 Oct 2020 20:18:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4225 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:19:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:19:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:19:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:19:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_summits.bed INFO @ Thu, 08 Oct 2020 20:19:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1389 records, 4 fields): 3 millis CompletedMACS2peakCalling