Job ID = 16434141 SRX = SRX15407774 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: 00:08:47 31369868 reads; of these: 31369868 (100.00%) were unpaired; of these: 1646575 (5.25%) aligned 0 times 26141681 (83.33%) aligned exactly 1 time 3581612 (11.42%) aligned >1 times 94.75% overall alignment rate Time searching: 00:08:47 Overall time: 00:08:47 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 16 files... [bam_rmdupse_core] 7936758 / 29723293 = 0.2670 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.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 @ Tue, 02 Aug 2022 10:03:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:03:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:03:35: 1000000 INFO @ Tue, 02 Aug 2022 10:03:42: 2000000 INFO @ Tue, 02 Aug 2022 10:03:49: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.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 @ Tue, 02 Aug 2022 10:03:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:03:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:03:56: 4000000 INFO @ Tue, 02 Aug 2022 10:04:05: 5000000 INFO @ Tue, 02 Aug 2022 10:04:06: 1000000 INFO @ Tue, 02 Aug 2022 10:04:14: 6000000 INFO @ Tue, 02 Aug 2022 10:04:14: 2000000 INFO @ Tue, 02 Aug 2022 10:04:22: 7000000 INFO @ Tue, 02 Aug 2022 10:04:23: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.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 @ Tue, 02 Aug 2022 10:04:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:04:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:04:31: 8000000 INFO @ Tue, 02 Aug 2022 10:04:32: 4000000 INFO @ Tue, 02 Aug 2022 10:04:35: 1000000 INFO @ Tue, 02 Aug 2022 10:04:40: 9000000 INFO @ Tue, 02 Aug 2022 10:04:41: 5000000 INFO @ Tue, 02 Aug 2022 10:04:43: 2000000 INFO @ Tue, 02 Aug 2022 10:04:49: 10000000 INFO @ Tue, 02 Aug 2022 10:04:49: 6000000 INFO @ Tue, 02 Aug 2022 10:04:52: 3000000 INFO @ Tue, 02 Aug 2022 10:04:57: 11000000 INFO @ Tue, 02 Aug 2022 10:04:58: 7000000 INFO @ Tue, 02 Aug 2022 10:05:00: 4000000 INFO @ Tue, 02 Aug 2022 10:05:06: 12000000 INFO @ Tue, 02 Aug 2022 10:05:07: 8000000 INFO @ Tue, 02 Aug 2022 10:05:09: 5000000 INFO @ Tue, 02 Aug 2022 10:05:15: 13000000 INFO @ Tue, 02 Aug 2022 10:05:16: 9000000 INFO @ Tue, 02 Aug 2022 10:05:17: 6000000 INFO @ Tue, 02 Aug 2022 10:05:23: 14000000 INFO @ Tue, 02 Aug 2022 10:05:25: 10000000 INFO @ Tue, 02 Aug 2022 10:05:26: 7000000 INFO @ Tue, 02 Aug 2022 10:05:32: 15000000 INFO @ Tue, 02 Aug 2022 10:05:34: 11000000 INFO @ Tue, 02 Aug 2022 10:05:34: 8000000 INFO @ Tue, 02 Aug 2022 10:05:40: 16000000 INFO @ Tue, 02 Aug 2022 10:05:42: 9000000 INFO @ Tue, 02 Aug 2022 10:05:42: 12000000 INFO @ Tue, 02 Aug 2022 10:05:48: 17000000 INFO @ Tue, 02 Aug 2022 10:05:51: 10000000 INFO @ Tue, 02 Aug 2022 10:05:51: 13000000 INFO @ Tue, 02 Aug 2022 10:05:57: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:05:59: 11000000 INFO @ Tue, 02 Aug 2022 10:06:00: 14000000 INFO @ Tue, 02 Aug 2022 10:06:05: 19000000 INFO @ Tue, 02 Aug 2022 10:06:07: 12000000 INFO @ Tue, 02 Aug 2022 10:06:09: 15000000 INFO @ Tue, 02 Aug 2022 10:06:13: 20000000 INFO @ Tue, 02 Aug 2022 10:06:16: 13000000 INFO @ Tue, 02 Aug 2022 10:06:17: 16000000 INFO @ Tue, 02 Aug 2022 10:06:21: 21000000 INFO @ Tue, 02 Aug 2022 10:06:24: 14000000 INFO @ Tue, 02 Aug 2022 10:06:26: 17000000 INFO @ Tue, 02 Aug 2022 10:06:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:06:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:06:27: #1 total tags in treatment: 21786535 INFO @ Tue, 02 Aug 2022 10:06:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:06:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:06:28: #1 tags after filtering in treatment: 21786535 INFO @ Tue, 02 Aug 2022 10:06:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:06:28: #1 finished! INFO @ Tue, 02 Aug 2022 10:06:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:06:29: #2 number of paired peaks: 599 WARNING @ Tue, 02 Aug 2022 10:06:29: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Tue, 02 Aug 2022 10:06:29: start model_add_line... INFO @ Tue, 02 Aug 2022 10:06:29: start X-correlation... INFO @ Tue, 02 Aug 2022 10:06:30: end of X-cor INFO @ Tue, 02 Aug 2022 10:06:30: #2 finished! INFO @ Tue, 02 Aug 2022 10:06:30: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 10:06:30: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 10:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.05_model.r INFO @ Tue, 02 Aug 2022 10:06:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:06:32: 15000000 INFO @ Tue, 02 Aug 2022 10:06:35: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:06:41: 16000000 INFO @ Tue, 02 Aug 2022 10:06:44: 19000000 INFO @ Tue, 02 Aug 2022 10:06:49: 17000000 INFO @ Tue, 02 Aug 2022 10:06:52: 20000000 INFO @ Tue, 02 Aug 2022 10:06:57: 18000000 INFO @ Tue, 02 Aug 2022 10:07:01: 21000000 INFO @ Tue, 02 Aug 2022 10:07:06: 19000000 INFO @ Tue, 02 Aug 2022 10:07:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:07:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:07:08: #1 total tags in treatment: 21786535 INFO @ Tue, 02 Aug 2022 10:07:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:08: #1 tags after filtering in treatment: 21786535 INFO @ Tue, 02 Aug 2022 10:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:08: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:10: #2 number of paired peaks: 599 WARNING @ Tue, 02 Aug 2022 10:07:10: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:10: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:10: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:10: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:10: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:10: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 10:07:10: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 10:07:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.10_model.r INFO @ Tue, 02 Aug 2022 10:07:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:07:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:07:13: 20000000 INFO @ Tue, 02 Aug 2022 10:07:20: 21000000 INFO @ Tue, 02 Aug 2022 10:07:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:07:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:07:25: #1 total tags in treatment: 21786535 INFO @ Tue, 02 Aug 2022 10:07:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:25: #1 tags after filtering in treatment: 21786535 INFO @ Tue, 02 Aug 2022 10:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:25: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:27: #2 number of paired peaks: 599 WARNING @ Tue, 02 Aug 2022 10:07:27: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:27: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:27: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:27: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:27: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:27: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 10:07:27: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 10:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.20_model.r INFO @ Tue, 02 Aug 2022 10:07:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:07:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:07:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:07:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.05_summits.bed INFO @ Tue, 02 Aug 2022 10:07:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14235 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:07:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:08:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.10_summits.bed INFO @ Tue, 02 Aug 2022 10:08:17: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10975 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407774/SRX15407774.20_summits.bed INFO @ Tue, 02 Aug 2022 10:08:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7617 records, 4 fields): 57 millis CompletedMACS2peakCalling