Job ID = 10166203 SRX = SRX8331152 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: 00:29:46 87376107 reads; of these: 87376107 (100.00%) were unpaired; of these: 862917 (0.99%) aligned 0 times 73134395 (83.70%) aligned exactly 1 time 13378795 (15.31%) aligned >1 times 99.01% overall alignment rate Time searching: 00:29:46 Overall time: 00:29:46 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 36 files... [bam_rmdupse_core] 68865564 / 86513190 = 0.7960 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 @ Thu, 08 Oct 2020 21:23:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.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, 08 Oct 2020 21:23:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:23:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:23:21: 1000000 INFO @ Thu, 08 Oct 2020 21:23:26: 2000000 INFO @ Thu, 08 Oct 2020 21:23:31: 3000000 INFO @ Thu, 08 Oct 2020 21:23:36: 4000000 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 @ Thu, 08 Oct 2020 21:23:42: 5000000 INFO @ Thu, 08 Oct 2020 21:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.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, 08 Oct 2020 21:23:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:23:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:23:47: 6000000 INFO @ Thu, 08 Oct 2020 21:23:51: 1000000 INFO @ Thu, 08 Oct 2020 21:23:52: 7000000 INFO @ Thu, 08 Oct 2020 21:23:57: 2000000 INFO @ Thu, 08 Oct 2020 21:23:57: 8000000 INFO @ Thu, 08 Oct 2020 21:24:02: 3000000 INFO @ Thu, 08 Oct 2020 21:24:03: 9000000 INFO @ Thu, 08 Oct 2020 21:24:07: 4000000 INFO @ Thu, 08 Oct 2020 21:24:08: 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 @ Thu, 08 Oct 2020 21:24:13: 5000000 INFO @ Thu, 08 Oct 2020 21:24:13: 11000000 INFO @ Thu, 08 Oct 2020 21:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.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, 08 Oct 2020 21:24:17: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:24:17: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:24:18: 6000000 INFO @ Thu, 08 Oct 2020 21:24:19: 12000000 INFO @ Thu, 08 Oct 2020 21:24:22: 1000000 INFO @ Thu, 08 Oct 2020 21:24:23: 7000000 INFO @ Thu, 08 Oct 2020 21:24:24: 13000000 INFO @ Thu, 08 Oct 2020 21:24:28: 2000000 INFO @ Thu, 08 Oct 2020 21:24:29: 8000000 INFO @ Thu, 08 Oct 2020 21:24:29: 14000000 INFO @ Thu, 08 Oct 2020 21:24:33: 3000000 INFO @ Thu, 08 Oct 2020 21:24:34: 9000000 INFO @ Thu, 08 Oct 2020 21:24:35: 15000000 INFO @ Thu, 08 Oct 2020 21:24:38: 4000000 INFO @ Thu, 08 Oct 2020 21:24:39: 10000000 INFO @ Thu, 08 Oct 2020 21:24:40: 16000000 INFO @ Thu, 08 Oct 2020 21:24:43: 5000000 INFO @ Thu, 08 Oct 2020 21:24:45: 11000000 INFO @ Thu, 08 Oct 2020 21:24:45: 17000000 INFO @ Thu, 08 Oct 2020 21:24:49: 6000000 INFO @ Thu, 08 Oct 2020 21:24:49: #1 tag size is determined as 72 bps INFO @ Thu, 08 Oct 2020 21:24:49: #1 tag size = 72 INFO @ Thu, 08 Oct 2020 21:24:49: #1 total tags in treatment: 17647626 INFO @ Thu, 08 Oct 2020 21:24:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:24:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:24:49: #1 tags after filtering in treatment: 17647626 INFO @ Thu, 08 Oct 2020 21:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:24:49: #1 finished! INFO @ Thu, 08 Oct 2020 21:24:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:24:50: 12000000 INFO @ Thu, 08 Oct 2020 21:24:50: #2 number of paired peaks: 503 WARNING @ Thu, 08 Oct 2020 21:24:50: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Thu, 08 Oct 2020 21:24:50: start model_add_line... INFO @ Thu, 08 Oct 2020 21:24:50: start X-correlation... INFO @ Thu, 08 Oct 2020 21:24:50: end of X-cor INFO @ Thu, 08 Oct 2020 21:24:50: #2 finished! INFO @ Thu, 08 Oct 2020 21:24:50: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 21:24:50: #2 alternative fragment length(s) may be 2,24,41 bps INFO @ Thu, 08 Oct 2020 21:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.05_model.r WARNING @ Thu, 08 Oct 2020 21:24:50: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:24:50: #2 You may need to consider one of the other alternative d(s): 2,24,41 WARNING @ Thu, 08 Oct 2020 21:24:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:24:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:24:54: 7000000 INFO @ Thu, 08 Oct 2020 21:24:55: 13000000 INFO @ Thu, 08 Oct 2020 21:24:59: 8000000 INFO @ Thu, 08 Oct 2020 21:25:00: 14000000 INFO @ Thu, 08 Oct 2020 21:25:04: 9000000 INFO @ Thu, 08 Oct 2020 21:25:06: 15000000 INFO @ Thu, 08 Oct 2020 21:25:10: 10000000 INFO @ Thu, 08 Oct 2020 21:25:11: 16000000 INFO @ Thu, 08 Oct 2020 21:25:15: 11000000 INFO @ Thu, 08 Oct 2020 21:25:16: 17000000 INFO @ Thu, 08 Oct 2020 21:25:20: #1 tag size is determined as 72 bps INFO @ Thu, 08 Oct 2020 21:25:20: #1 tag size = 72 INFO @ Thu, 08 Oct 2020 21:25:20: #1 total tags in treatment: 17647626 INFO @ Thu, 08 Oct 2020 21:25:20: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:25:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:25:20: #1 tags after filtering in treatment: 17647626 INFO @ Thu, 08 Oct 2020 21:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:25:20: #1 finished! INFO @ Thu, 08 Oct 2020 21:25:20: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:25:20: 12000000 INFO @ Thu, 08 Oct 2020 21:25:21: #2 number of paired peaks: 503 WARNING @ Thu, 08 Oct 2020 21:25:21: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Thu, 08 Oct 2020 21:25:21: start model_add_line... INFO @ Thu, 08 Oct 2020 21:25:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:25:21: start X-correlation... INFO @ Thu, 08 Oct 2020 21:25:21: end of X-cor INFO @ Thu, 08 Oct 2020 21:25:21: #2 finished! INFO @ Thu, 08 Oct 2020 21:25:21: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 21:25:21: #2 alternative fragment length(s) may be 2,24,41 bps INFO @ Thu, 08 Oct 2020 21:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.10_model.r WARNING @ Thu, 08 Oct 2020 21:25:21: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:25:21: #2 You may need to consider one of the other alternative d(s): 2,24,41 WARNING @ Thu, 08 Oct 2020 21:25:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:25:21: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:25:25: 13000000 INFO @ Thu, 08 Oct 2020 21:25:30: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:25:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:25:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:25:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.05_summits.bed INFO @ Thu, 08 Oct 2020 21:25:35: Done! INFO @ Thu, 08 Oct 2020 21:25:35: 15000000 INFO @ Thu, 08 Oct 2020 21:25:40: 16000000 INFO @ Thu, 08 Oct 2020 21:25:46: 17000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:25:49: #1 tag size is determined as 72 bps INFO @ Thu, 08 Oct 2020 21:25:49: #1 tag size = 72 INFO @ Thu, 08 Oct 2020 21:25:49: #1 total tags in treatment: 17647626 INFO @ Thu, 08 Oct 2020 21:25:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:25:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:25:49: #1 tags after filtering in treatment: 17647626 INFO @ Thu, 08 Oct 2020 21:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:25:49: #1 finished! INFO @ Thu, 08 Oct 2020 21:25:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:25:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:25:50: #2 number of paired peaks: 503 WARNING @ Thu, 08 Oct 2020 21:25:50: Fewer paired peaks (503) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 503 pairs to build model! INFO @ Thu, 08 Oct 2020 21:25:50: start model_add_line... INFO @ Thu, 08 Oct 2020 21:25:51: start X-correlation... INFO @ Thu, 08 Oct 2020 21:25:51: end of X-cor INFO @ Thu, 08 Oct 2020 21:25:51: #2 finished! INFO @ Thu, 08 Oct 2020 21:25:51: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 21:25:51: #2 alternative fragment length(s) may be 2,24,41 bps INFO @ Thu, 08 Oct 2020 21:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.20_model.r WARNING @ Thu, 08 Oct 2020 21:25:51: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:25:51: #2 You may need to consider one of the other alternative d(s): 2,24,41 WARNING @ Thu, 08 Oct 2020 21:25:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:25:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:26:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.10_summits.bed INFO @ Thu, 08 Oct 2020 21:26:04: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:26:20: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331152/SRX8331152.20_summits.bed INFO @ Thu, 08 Oct 2020 21:26:35: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling