Job ID = 6529110 SRX = SRX5402765 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: 00:06:40 28004945 reads; of these: 28004945 (100.00%) were unpaired; of these: 1171396 (4.18%) aligned 0 times 22114766 (78.97%) aligned exactly 1 time 4718783 (16.85%) aligned >1 times 95.82% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 7442469 / 26833549 = 0.2774 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 @ Tue, 30 Jun 2020 01:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.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, 30 Jun 2020 01:23:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:23:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:24:04: 1000000 INFO @ Tue, 30 Jun 2020 01:24:10: 2000000 INFO @ Tue, 30 Jun 2020 01:24:15: 3000000 INFO @ Tue, 30 Jun 2020 01:24:21: 4000000 INFO @ Tue, 30 Jun 2020 01:24:26: 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 @ Tue, 30 Jun 2020 01:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.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, 30 Jun 2020 01:24:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:24:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:24:32: 6000000 INFO @ Tue, 30 Jun 2020 01:24:34: 1000000 INFO @ Tue, 30 Jun 2020 01:24:37: 7000000 INFO @ Tue, 30 Jun 2020 01:24:40: 2000000 INFO @ Tue, 30 Jun 2020 01:24:43: 8000000 INFO @ Tue, 30 Jun 2020 01:24:45: 3000000 INFO @ Tue, 30 Jun 2020 01:24:49: 9000000 INFO @ Tue, 30 Jun 2020 01:24:51: 4000000 INFO @ Tue, 30 Jun 2020 01:24:54: 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 @ Tue, 30 Jun 2020 01:24:56: 5000000 INFO @ Tue, 30 Jun 2020 01:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.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, 30 Jun 2020 01:24:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:24:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:25:00: 11000000 INFO @ Tue, 30 Jun 2020 01:25:02: 6000000 INFO @ Tue, 30 Jun 2020 01:25:04: 1000000 INFO @ Tue, 30 Jun 2020 01:25:06: 12000000 INFO @ Tue, 30 Jun 2020 01:25:08: 7000000 INFO @ Tue, 30 Jun 2020 01:25:10: 2000000 INFO @ Tue, 30 Jun 2020 01:25:12: 13000000 INFO @ Tue, 30 Jun 2020 01:25:14: 8000000 INFO @ Tue, 30 Jun 2020 01:25:16: 3000000 INFO @ Tue, 30 Jun 2020 01:25:18: 14000000 INFO @ Tue, 30 Jun 2020 01:25:20: 9000000 INFO @ Tue, 30 Jun 2020 01:25:21: 4000000 INFO @ Tue, 30 Jun 2020 01:25:24: 15000000 INFO @ Tue, 30 Jun 2020 01:25:26: 10000000 INFO @ Tue, 30 Jun 2020 01:25:27: 5000000 INFO @ Tue, 30 Jun 2020 01:25:30: 16000000 INFO @ Tue, 30 Jun 2020 01:25:32: 11000000 INFO @ Tue, 30 Jun 2020 01:25:33: 6000000 INFO @ Tue, 30 Jun 2020 01:25:36: 17000000 INFO @ Tue, 30 Jun 2020 01:25:38: 12000000 INFO @ Tue, 30 Jun 2020 01:25:38: 7000000 INFO @ Tue, 30 Jun 2020 01:25:42: 18000000 INFO @ Tue, 30 Jun 2020 01:25:44: 13000000 INFO @ Tue, 30 Jun 2020 01:25:44: 8000000 INFO @ Tue, 30 Jun 2020 01:25:48: 19000000 INFO @ Tue, 30 Jun 2020 01:25:50: 9000000 INFO @ Tue, 30 Jun 2020 01:25:50: 14000000 INFO @ Tue, 30 Jun 2020 01:25:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:25:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:25:51: #1 total tags in treatment: 19391080 INFO @ Tue, 30 Jun 2020 01:25:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:25:51: #1 tags after filtering in treatment: 19391080 INFO @ Tue, 30 Jun 2020 01:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:25:51: #1 finished! INFO @ Tue, 30 Jun 2020 01:25:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:25:52: #2 number of paired peaks: 294 WARNING @ Tue, 30 Jun 2020 01:25:52: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Tue, 30 Jun 2020 01:25:52: start model_add_line... INFO @ Tue, 30 Jun 2020 01:25:53: start X-correlation... INFO @ Tue, 30 Jun 2020 01:25:53: end of X-cor INFO @ Tue, 30 Jun 2020 01:25:53: #2 finished! INFO @ Tue, 30 Jun 2020 01:25:53: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:25:53: #2 alternative fragment length(s) may be 1,538 bps INFO @ Tue, 30 Jun 2020 01:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.05_model.r WARNING @ Tue, 30 Jun 2020 01:25:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:25:53: #2 You may need to consider one of the other alternative d(s): 1,538 WARNING @ Tue, 30 Jun 2020 01:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:25:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:25:56: 10000000 INFO @ Tue, 30 Jun 2020 01:25:56: 15000000 INFO @ Tue, 30 Jun 2020 01:26:01: 16000000 INFO @ Tue, 30 Jun 2020 01:26:01: 11000000 INFO @ Tue, 30 Jun 2020 01:26:07: 17000000 INFO @ Tue, 30 Jun 2020 01:26:07: 12000000 INFO @ Tue, 30 Jun 2020 01:26:13: 18000000 INFO @ Tue, 30 Jun 2020 01:26:13: 13000000 INFO @ Tue, 30 Jun 2020 01:26:18: 19000000 INFO @ Tue, 30 Jun 2020 01:26:18: 14000000 INFO @ Tue, 30 Jun 2020 01:26:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:26:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:26:21: #1 total tags in treatment: 19391080 INFO @ Tue, 30 Jun 2020 01:26:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:26:21: #1 tags after filtering in treatment: 19391080 INFO @ Tue, 30 Jun 2020 01:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:26:21: #1 finished! INFO @ Tue, 30 Jun 2020 01:26:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:26:22: #2 number of paired peaks: 294 WARNING @ Tue, 30 Jun 2020 01:26:22: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Tue, 30 Jun 2020 01:26:22: start model_add_line... INFO @ Tue, 30 Jun 2020 01:26:22: start X-correlation... INFO @ Tue, 30 Jun 2020 01:26:22: end of X-cor INFO @ Tue, 30 Jun 2020 01:26:22: #2 finished! INFO @ Tue, 30 Jun 2020 01:26:22: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:26:22: #2 alternative fragment length(s) may be 1,538 bps INFO @ Tue, 30 Jun 2020 01:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.10_model.r WARNING @ Tue, 30 Jun 2020 01:26:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:26:22: #2 You may need to consider one of the other alternative d(s): 1,538 WARNING @ Tue, 30 Jun 2020 01:26:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:26:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:26:24: 15000000 INFO @ Tue, 30 Jun 2020 01:26:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:26:30: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:26:35: 17000000 INFO @ Tue, 30 Jun 2020 01:26:41: 18000000 INFO @ Tue, 30 Jun 2020 01:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.05_summits.bed INFO @ Tue, 30 Jun 2020 01:26:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:26:47: 19000000 INFO @ Tue, 30 Jun 2020 01:26:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:26:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:26:49: #1 total tags in treatment: 19391080 INFO @ Tue, 30 Jun 2020 01:26:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:26:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:26:50: #1 tags after filtering in treatment: 19391080 INFO @ Tue, 30 Jun 2020 01:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:26:50: #1 finished! INFO @ Tue, 30 Jun 2020 01:26:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:26:51: #2 number of paired peaks: 294 WARNING @ Tue, 30 Jun 2020 01:26:51: Fewer paired peaks (294) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 294 pairs to build model! INFO @ Tue, 30 Jun 2020 01:26:51: start model_add_line... INFO @ Tue, 30 Jun 2020 01:26:51: start X-correlation... INFO @ Tue, 30 Jun 2020 01:26:51: end of X-cor INFO @ Tue, 30 Jun 2020 01:26:51: #2 finished! INFO @ Tue, 30 Jun 2020 01:26:51: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:26:51: #2 alternative fragment length(s) may be 1,538 bps INFO @ Tue, 30 Jun 2020 01:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.20_model.r WARNING @ Tue, 30 Jun 2020 01:26:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:26:51: #2 You may need to consider one of the other alternative d(s): 1,538 WARNING @ Tue, 30 Jun 2020 01:26:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:26:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:27:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.10_summits.bed INFO @ Tue, 30 Jun 2020 01:27:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:27:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402765/SRX5402765.20_summits.bed INFO @ Tue, 30 Jun 2020 01:27:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling