Job ID = 6529100 SRX = SRX3043410 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: 00:05:05 17754014 reads; of these: 17754014 (100.00%) were unpaired; of these: 404924 (2.28%) aligned 0 times 14872513 (83.77%) aligned exactly 1 time 2476577 (13.95%) aligned >1 times 97.72% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 2365287 / 17349090 = 0.1363 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 01:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.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 01:28:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:28:46: 1000000 INFO @ Tue, 30 Jun 2020 01:28:53: 2000000 INFO @ Tue, 30 Jun 2020 01:29:01: 3000000 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 01:29:08: 4000000 INFO @ Tue, 30 Jun 2020 01:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.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 01:29:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:16: 5000000 INFO @ Tue, 30 Jun 2020 01:29:17: 1000000 INFO @ Tue, 30 Jun 2020 01:29:24: 6000000 INFO @ Tue, 30 Jun 2020 01:29:25: 2000000 INFO @ Tue, 30 Jun 2020 01:29:32: 7000000 INFO @ Tue, 30 Jun 2020 01:29:33: 3000000 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 01:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.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 01:29:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:41: 8000000 INFO @ Tue, 30 Jun 2020 01:29:42: 4000000 INFO @ Tue, 30 Jun 2020 01:29:47: 1000000 INFO @ Tue, 30 Jun 2020 01:29:50: 9000000 INFO @ Tue, 30 Jun 2020 01:29:51: 5000000 INFO @ Tue, 30 Jun 2020 01:29:55: 2000000 INFO @ Tue, 30 Jun 2020 01:29:59: 10000000 INFO @ Tue, 30 Jun 2020 01:30:00: 6000000 INFO @ Tue, 30 Jun 2020 01:30:03: 3000000 INFO @ Tue, 30 Jun 2020 01:30:08: 11000000 INFO @ Tue, 30 Jun 2020 01:30:09: 7000000 INFO @ Tue, 30 Jun 2020 01:30:11: 4000000 INFO @ Tue, 30 Jun 2020 01:30:18: 12000000 INFO @ Tue, 30 Jun 2020 01:30:19: 8000000 INFO @ Tue, 30 Jun 2020 01:30:19: 5000000 INFO @ Tue, 30 Jun 2020 01:30:27: 13000000 INFO @ Tue, 30 Jun 2020 01:30:27: 6000000 INFO @ Tue, 30 Jun 2020 01:30:28: 9000000 INFO @ Tue, 30 Jun 2020 01:30:35: 7000000 INFO @ Tue, 30 Jun 2020 01:30:36: 14000000 INFO @ Tue, 30 Jun 2020 01:30:37: 10000000 INFO @ Tue, 30 Jun 2020 01:30:44: 8000000 INFO @ Tue, 30 Jun 2020 01:30:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:30:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:30:45: #1 total tags in treatment: 14983803 INFO @ Tue, 30 Jun 2020 01:30:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:45: #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 01:30:45: #1 tags after filtering in treatment: 14983803 INFO @ Tue, 30 Jun 2020 01:30:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:45: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:46: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 01:30:46: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:46: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:46: 11000000 INFO @ Tue, 30 Jun 2020 01:30:46: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:46: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:46: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:46: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:30:46: #2 alternative fragment length(s) may be 1,10,47,445,522,586 bps INFO @ Tue, 30 Jun 2020 01:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.05_model.r WARNING @ Tue, 30 Jun 2020 01:30:46: #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 01:30:46: #2 You may need to consider one of the other alternative d(s): 1,10,47,445,522,586 WARNING @ Tue, 30 Jun 2020 01:30:46: #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 01:30:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:52: 9000000 INFO @ Tue, 30 Jun 2020 01:30:55: 12000000 INFO @ Tue, 30 Jun 2020 01:31:00: 10000000 INFO @ Tue, 30 Jun 2020 01:31:03: 13000000 INFO @ Tue, 30 Jun 2020 01:31:08: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:31:11: 14000000 INFO @ Tue, 30 Jun 2020 01:31:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:16: 12000000 INFO @ Tue, 30 Jun 2020 01:31:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:20: #1 total tags in treatment: 14983803 INFO @ Tue, 30 Jun 2020 01:31:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:20: #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 01:31:20: #1 tags after filtering in treatment: 14983803 INFO @ Tue, 30 Jun 2020 01:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:20: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:21: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 01:31:21: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:21: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:21: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:21: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:21: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:21: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:31:21: #2 alternative fragment length(s) may be 1,10,47,445,522,586 bps INFO @ Tue, 30 Jun 2020 01:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.10_model.r WARNING @ Tue, 30 Jun 2020 01:31:21: #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 01:31:21: #2 You may need to consider one of the other alternative d(s): 1,10,47,445,522,586 WARNING @ Tue, 30 Jun 2020 01:31:21: #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 01:31:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:31:24: 13000000 INFO @ Tue, 30 Jun 2020 01:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.05_summits.bed INFO @ Tue, 30 Jun 2020 01:31:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:30: 14000000 INFO @ Tue, 30 Jun 2020 01:31:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:37: #1 total tags in treatment: 14983803 INFO @ Tue, 30 Jun 2020 01:31:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:37: #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 01:31:38: #1 tags after filtering in treatment: 14983803 INFO @ Tue, 30 Jun 2020 01:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:38: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:39: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 01:31:39: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:39: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:39: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:39: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:39: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:39: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:31:39: #2 alternative fragment length(s) may be 1,10,47,445,522,586 bps INFO @ Tue, 30 Jun 2020 01:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.20_model.r WARNING @ Tue, 30 Jun 2020 01:31:39: #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 01:31:39: #2 You may need to consider one of the other alternative d(s): 1,10,47,445,522,586 WARNING @ Tue, 30 Jun 2020 01:31:39: #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 01:31:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:31:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:31:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.10_summits.bed INFO @ Tue, 30 Jun 2020 01:31:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:32:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:32:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:32:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:32:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043410/SRX3043410.20_summits.bed INFO @ Tue, 30 Jun 2020 01:32:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling