Job ID = 16433628 SRX = SRX15407780 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: 00:04:45 16524259 reads; of these: 16524259 (100.00%) were unpaired; of these: 1988661 (12.03%) aligned 0 times 12589157 (76.19%) aligned exactly 1 time 1946441 (11.78%) aligned >1 times 87.97% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 2004625 / 14535598 = 0.1379 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 09:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.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 09:52:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:52:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:52:11: 1000000 INFO @ Tue, 02 Aug 2022 09:52:17: 2000000 INFO @ Tue, 02 Aug 2022 09:52:23: 3000000 INFO @ Tue, 02 Aug 2022 09:52:28: 4000000 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 09:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.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 09:52:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:52:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:52:35: 5000000 INFO @ Tue, 02 Aug 2022 09:52:41: 6000000 INFO @ Tue, 02 Aug 2022 09:52:41: 1000000 INFO @ Tue, 02 Aug 2022 09:52:48: 7000000 INFO @ Tue, 02 Aug 2022 09:52:48: 2000000 INFO @ Tue, 02 Aug 2022 09:52:54: 8000000 INFO @ Tue, 02 Aug 2022 09:52:54: 3000000 INFO @ Tue, 02 Aug 2022 09:53:01: 9000000 INFO @ Tue, 02 Aug 2022 09:53:01: 4000000 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 09:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.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 09:53:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:53:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:53:07: 5000000 INFO @ Tue, 02 Aug 2022 09:53:07: 10000000 INFO @ Tue, 02 Aug 2022 09:53:11: 1000000 INFO @ Tue, 02 Aug 2022 09:53:14: 6000000 INFO @ Tue, 02 Aug 2022 09:53:14: 11000000 INFO @ Tue, 02 Aug 2022 09:53:18: 2000000 INFO @ Tue, 02 Aug 2022 09:53:20: 7000000 INFO @ Tue, 02 Aug 2022 09:53:21: 12000000 INFO @ Tue, 02 Aug 2022 09:53:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:53:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:53:25: #1 total tags in treatment: 12530973 INFO @ Tue, 02 Aug 2022 09:53:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:25: #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 09:53:25: #1 tags after filtering in treatment: 12530973 INFO @ Tue, 02 Aug 2022 09:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:25: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:25: 3000000 INFO @ Tue, 02 Aug 2022 09:53:26: #2 number of paired peaks: 485 WARNING @ Tue, 02 Aug 2022 09:53:26: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:26: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:26: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:26: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:26: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:26: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 09:53:26: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 09:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.05_model.r INFO @ Tue, 02 Aug 2022 09:53:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:26: 8000000 INFO @ Tue, 02 Aug 2022 09:53:31: 4000000 INFO @ Tue, 02 Aug 2022 09:53:33: 9000000 INFO @ Tue, 02 Aug 2022 09:53:38: 5000000 INFO @ Tue, 02 Aug 2022 09:53:39: 10000000 INFO @ Tue, 02 Aug 2022 09:53:44: 6000000 INFO @ Tue, 02 Aug 2022 09:53:45: 11000000 INFO @ Tue, 02 Aug 2022 09:53:51: 7000000 INFO @ Tue, 02 Aug 2022 09:53:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:52: 12000000 INFO @ Tue, 02 Aug 2022 09:53:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:53:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:53:55: #1 total tags in treatment: 12530973 INFO @ Tue, 02 Aug 2022 09:53:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:55: #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 09:53:55: #1 tags after filtering in treatment: 12530973 INFO @ Tue, 02 Aug 2022 09:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:55: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:56: #2 number of paired peaks: 485 WARNING @ Tue, 02 Aug 2022 09:53:56: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:56: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:56: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:56: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:56: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:56: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 09:53:56: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 09:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.10_model.r INFO @ Tue, 02 Aug 2022 09:53:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:57: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:54:03: 9000000 INFO @ Tue, 02 Aug 2022 09:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.05_summits.bed INFO @ Tue, 02 Aug 2022 09:54:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6290 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:08: 10000000 INFO @ Tue, 02 Aug 2022 09:54:14: 11000000 INFO @ Tue, 02 Aug 2022 09:54:20: 12000000 INFO @ Tue, 02 Aug 2022 09:54:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:23: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:54:23: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:54:23: #1 total tags in treatment: 12530973 INFO @ Tue, 02 Aug 2022 09:54:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:54:23: #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 09:54:23: #1 tags after filtering in treatment: 12530973 INFO @ Tue, 02 Aug 2022 09:54:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:54:23: #1 finished! INFO @ Tue, 02 Aug 2022 09:54:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:54:24: #2 number of paired peaks: 485 WARNING @ Tue, 02 Aug 2022 09:54:24: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Tue, 02 Aug 2022 09:54:24: start model_add_line... INFO @ Tue, 02 Aug 2022 09:54:24: start X-correlation... INFO @ Tue, 02 Aug 2022 09:54:24: end of X-cor INFO @ Tue, 02 Aug 2022 09:54:24: #2 finished! INFO @ Tue, 02 Aug 2022 09:54:24: #2 predicted fragment length is 160 bps INFO @ Tue, 02 Aug 2022 09:54:24: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 02 Aug 2022 09:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.20_model.r INFO @ Tue, 02 Aug 2022 09:54:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:54:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:54:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.10_summits.bed INFO @ Tue, 02 Aug 2022 09:54:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4169 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407780/SRX15407780.20_summits.bed INFO @ Tue, 02 Aug 2022 09:55:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2290 records, 4 fields): 36 millis CompletedMACS2peakCalling