Job ID = 14160308 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: 00:04:20 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: 00:04:20 Overall time: 00:04:20 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:28:27: # 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, 09 Dec 2021 01:28:27: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:28:27: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:28:33: 1000000 INFO @ Thu, 09 Dec 2021 01:28:38: 2000000 INFO @ Thu, 09 Dec 2021 01:28:43: 3000000 INFO @ Thu, 09 Dec 2021 01:28:48: 4000000 INFO @ Thu, 09 Dec 2021 01:28:54: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:28:57: # 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, 09 Dec 2021 01:28:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:28:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:28:59: 6000000 INFO @ Thu, 09 Dec 2021 01:29:03: 1000000 INFO @ Thu, 09 Dec 2021 01:29:05: 7000000 INFO @ Thu, 09 Dec 2021 01:29:09: 2000000 INFO @ Thu, 09 Dec 2021 01:29:11: 8000000 INFO @ Thu, 09 Dec 2021 01:29:15: 3000000 INFO @ Thu, 09 Dec 2021 01:29:17: 9000000 INFO @ Thu, 09 Dec 2021 01:29:21: 4000000 INFO @ Thu, 09 Dec 2021 01:29:22: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 01:29:27: 5000000 INFO @ Thu, 09 Dec 2021 01:29:27: # 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, 09 Dec 2021 01:29:27: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:29:27: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:29:28: 11000000 INFO @ Thu, 09 Dec 2021 01:29:33: 6000000 INFO @ Thu, 09 Dec 2021 01:29:33: 1000000 INFO @ Thu, 09 Dec 2021 01:29:34: 12000000 INFO @ Thu, 09 Dec 2021 01:29:39: 7000000 INFO @ Thu, 09 Dec 2021 01:29:39: 2000000 INFO @ Thu, 09 Dec 2021 01:29:40: 13000000 INFO @ Thu, 09 Dec 2021 01:29:45: 8000000 INFO @ Thu, 09 Dec 2021 01:29:45: 3000000 INFO @ Thu, 09 Dec 2021 01:29:46: 14000000 INFO @ Thu, 09 Dec 2021 01:29:51: 9000000 INFO @ Thu, 09 Dec 2021 01:29:51: 4000000 INFO @ Thu, 09 Dec 2021 01:29:52: 15000000 INFO @ Thu, 09 Dec 2021 01:29:57: 10000000 INFO @ Thu, 09 Dec 2021 01:29:57: 5000000 INFO @ Thu, 09 Dec 2021 01:29:58: 16000000 INFO @ Thu, 09 Dec 2021 01:30:02: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 01:30:02: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 01:30:02: #1 total tags in treatment: 16715617 INFO @ Thu, 09 Dec 2021 01:30:02: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:30:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:30:03: #1 tags after filtering in treatment: 16715617 INFO @ Thu, 09 Dec 2021 01:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:30:03: #1 finished! INFO @ Thu, 09 Dec 2021 01:30:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:30:03: 11000000 INFO @ Thu, 09 Dec 2021 01:30:03: 6000000 INFO @ Thu, 09 Dec 2021 01:30:04: #2 number of paired peaks: 199 WARNING @ Thu, 09 Dec 2021 01:30:04: 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, 09 Dec 2021 01:30:04: start model_add_line... INFO @ Thu, 09 Dec 2021 01:30:04: start X-correlation... INFO @ Thu, 09 Dec 2021 01:30:04: end of X-cor INFO @ Thu, 09 Dec 2021 01:30:04: #2 finished! INFO @ Thu, 09 Dec 2021 01:30:04: #2 predicted fragment length is 122 bps INFO @ Thu, 09 Dec 2021 01:30:04: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 09 Dec 2021 01:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_model.r INFO @ Thu, 09 Dec 2021 01:30:04: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:30:09: 12000000 INFO @ Thu, 09 Dec 2021 01:30:09: 7000000 INFO @ Thu, 09 Dec 2021 01:30:15: 13000000 INFO @ Thu, 09 Dec 2021 01:30:15: 8000000 INFO @ Thu, 09 Dec 2021 01:30:21: 14000000 INFO @ Thu, 09 Dec 2021 01:30:21: 9000000 INFO @ Thu, 09 Dec 2021 01:30:27: 15000000 INFO @ Thu, 09 Dec 2021 01:30:27: 10000000 INFO @ Thu, 09 Dec 2021 01:30:33: 16000000 INFO @ Thu, 09 Dec 2021 01:30:33: 11000000 INFO @ Thu, 09 Dec 2021 01:30:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:30:37: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 01:30:37: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 01:30:37: #1 total tags in treatment: 16715617 INFO @ Thu, 09 Dec 2021 01:30:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:30:38: #1 tags after filtering in treatment: 16715617 INFO @ Thu, 09 Dec 2021 01:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:30:38: #1 finished! INFO @ Thu, 09 Dec 2021 01:30:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:30:38: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:30:39: #2 number of paired peaks: 199 WARNING @ Thu, 09 Dec 2021 01:30:39: 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, 09 Dec 2021 01:30:39: start model_add_line... INFO @ Thu, 09 Dec 2021 01:30:39: start X-correlation... INFO @ Thu, 09 Dec 2021 01:30:39: end of X-cor INFO @ Thu, 09 Dec 2021 01:30:39: #2 finished! INFO @ Thu, 09 Dec 2021 01:30:39: #2 predicted fragment length is 122 bps INFO @ Thu, 09 Dec 2021 01:30:39: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 09 Dec 2021 01:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_model.r INFO @ Thu, 09 Dec 2021 01:30:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:30:39: 12000000 INFO @ Thu, 09 Dec 2021 01:30:45: 13000000 INFO @ Thu, 09 Dec 2021 01:30:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:30:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:30:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.05_summits.bed INFO @ Thu, 09 Dec 2021 01:30:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7499 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:30:51: 14000000 INFO @ Thu, 09 Dec 2021 01:30:56: 15000000 INFO @ Thu, 09 Dec 2021 01:31:01: 16000000 INFO @ Thu, 09 Dec 2021 01:31:05: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 01:31:05: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 01:31:05: #1 total tags in treatment: 16715617 INFO @ Thu, 09 Dec 2021 01:31:05: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:31:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:31:05: #1 tags after filtering in treatment: 16715617 INFO @ Thu, 09 Dec 2021 01:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 01:31:05: #1 finished! INFO @ Thu, 09 Dec 2021 01:31:05: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:31:06: #2 number of paired peaks: 199 WARNING @ Thu, 09 Dec 2021 01:31:06: 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, 09 Dec 2021 01:31:06: start model_add_line... INFO @ Thu, 09 Dec 2021 01:31:06: start X-correlation... INFO @ Thu, 09 Dec 2021 01:31:06: end of X-cor INFO @ Thu, 09 Dec 2021 01:31:06: #2 finished! INFO @ Thu, 09 Dec 2021 01:31:06: #2 predicted fragment length is 122 bps INFO @ Thu, 09 Dec 2021 01:31:06: #2 alternative fragment length(s) may be 3,67,88,122 bps INFO @ Thu, 09 Dec 2021 01:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_model.r INFO @ Thu, 09 Dec 2021 01:31:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:31:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:31:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:31:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:31:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:31:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.10_summits.bed INFO @ Thu, 09 Dec 2021 01:31:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4225 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:31:38: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832065/SRX8832065.20_summits.bed INFO @ Thu, 09 Dec 2021 01:31:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1389 records, 4 fields): 3 millis CompletedMACS2peakCalling