Job ID = 6529107 SRX = SRX494841 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: 00:04:01 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255393 (1.19%) aligned 0 times 17821529 (82.85%) aligned exactly 1 time 3432687 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 3667422 / 21254216 = 0.1726 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 01:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.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 01:25:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:25:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:25:42: 1000000 INFO @ Tue, 30 Jun 2020 01:25:46: 2000000 INFO @ Tue, 30 Jun 2020 01:25:51: 3000000 INFO @ Tue, 30 Jun 2020 01:25:56: 4000000 INFO @ Tue, 30 Jun 2020 01:26:00: 5000000 INFO @ Tue, 30 Jun 2020 01:26:05: 6000000 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 01:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.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 01:26:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:26:10: 7000000 INFO @ Tue, 30 Jun 2020 01:26:12: 1000000 INFO @ Tue, 30 Jun 2020 01:26:14: 8000000 INFO @ Tue, 30 Jun 2020 01:26:17: 2000000 INFO @ Tue, 30 Jun 2020 01:26:19: 9000000 INFO @ Tue, 30 Jun 2020 01:26:21: 3000000 INFO @ Tue, 30 Jun 2020 01:26:24: 10000000 INFO @ Tue, 30 Jun 2020 01:26:26: 4000000 INFO @ Tue, 30 Jun 2020 01:26:29: 11000000 INFO @ Tue, 30 Jun 2020 01:26:31: 5000000 INFO @ Tue, 30 Jun 2020 01:26:33: 12000000 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 01:26:35: 6000000 INFO @ Tue, 30 Jun 2020 01:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.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 01:26:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:26:38: 13000000 INFO @ Tue, 30 Jun 2020 01:26:40: 7000000 INFO @ Tue, 30 Jun 2020 01:26:42: 1000000 INFO @ Tue, 30 Jun 2020 01:26:43: 14000000 INFO @ Tue, 30 Jun 2020 01:26:45: 8000000 INFO @ Tue, 30 Jun 2020 01:26:47: 2000000 INFO @ Tue, 30 Jun 2020 01:26:48: 15000000 INFO @ Tue, 30 Jun 2020 01:26:50: 9000000 INFO @ Tue, 30 Jun 2020 01:26:52: 3000000 INFO @ Tue, 30 Jun 2020 01:26:52: 16000000 INFO @ Tue, 30 Jun 2020 01:26:54: 10000000 INFO @ Tue, 30 Jun 2020 01:26:56: 4000000 INFO @ Tue, 30 Jun 2020 01:26:57: 17000000 INFO @ Tue, 30 Jun 2020 01:26:59: 11000000 INFO @ Tue, 30 Jun 2020 01:27:00: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:27:00: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:27:00: #1 total tags in treatment: 17586794 INFO @ Tue, 30 Jun 2020 01:27:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:27:00: #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 01:27:00: #1 tags after filtering in treatment: 17586794 INFO @ Tue, 30 Jun 2020 01:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:27:00: #1 finished! INFO @ Tue, 30 Jun 2020 01:27:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:27:01: 5000000 INFO @ Tue, 30 Jun 2020 01:27:01: #2 number of paired peaks: 223 WARNING @ Tue, 30 Jun 2020 01:27:01: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Tue, 30 Jun 2020 01:27:01: start model_add_line... INFO @ Tue, 30 Jun 2020 01:27:02: start X-correlation... INFO @ Tue, 30 Jun 2020 01:27:02: end of X-cor INFO @ Tue, 30 Jun 2020 01:27:02: #2 finished! INFO @ Tue, 30 Jun 2020 01:27:02: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:27:02: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 30 Jun 2020 01:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.05_model.r WARNING @ Tue, 30 Jun 2020 01:27:02: #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 01:27:02: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 30 Jun 2020 01:27:02: #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 01:27:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:27:04: 12000000 INFO @ Tue, 30 Jun 2020 01:27:06: 6000000 INFO @ Tue, 30 Jun 2020 01:27:09: 13000000 INFO @ Tue, 30 Jun 2020 01:27:11: 7000000 INFO @ Tue, 30 Jun 2020 01:27:13: 14000000 INFO @ Tue, 30 Jun 2020 01:27:16: 8000000 INFO @ Tue, 30 Jun 2020 01:27:18: 15000000 INFO @ Tue, 30 Jun 2020 01:27:21: 9000000 INFO @ Tue, 30 Jun 2020 01:27:23: 16000000 INFO @ Tue, 30 Jun 2020 01:27:26: 10000000 INFO @ Tue, 30 Jun 2020 01:27:28: 17000000 INFO @ Tue, 30 Jun 2020 01:27:30: 11000000 INFO @ Tue, 30 Jun 2020 01:27:31: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:27:31: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:27:31: #1 total tags in treatment: 17586794 INFO @ Tue, 30 Jun 2020 01:27:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:27:31: #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 01:27:31: #1 tags after filtering in treatment: 17586794 INFO @ Tue, 30 Jun 2020 01:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:27:31: #1 finished! INFO @ Tue, 30 Jun 2020 01:27:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:27:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:27:32: #2 number of paired peaks: 223 WARNING @ Tue, 30 Jun 2020 01:27:32: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Tue, 30 Jun 2020 01:27:32: start model_add_line... INFO @ Tue, 30 Jun 2020 01:27:32: start X-correlation... INFO @ Tue, 30 Jun 2020 01:27:32: end of X-cor INFO @ Tue, 30 Jun 2020 01:27:32: #2 finished! INFO @ Tue, 30 Jun 2020 01:27:32: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:27:32: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 30 Jun 2020 01:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.10_model.r WARNING @ Tue, 30 Jun 2020 01:27:32: #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 01:27:32: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 30 Jun 2020 01:27:32: #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 01:27:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:27:35: 12000000 INFO @ Tue, 30 Jun 2020 01:27:40: 13000000 INFO @ Tue, 30 Jun 2020 01:27:45: 14000000 INFO @ Tue, 30 Jun 2020 01:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.05_summits.bed INFO @ Tue, 30 Jun 2020 01:27:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:27:50: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:27:54: 16000000 INFO @ Tue, 30 Jun 2020 01:27:59: 17000000 INFO @ Tue, 30 Jun 2020 01:28:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:28:02: #1 tag size is determined as 42 bps INFO @ Tue, 30 Jun 2020 01:28:02: #1 tag size = 42 INFO @ Tue, 30 Jun 2020 01:28:02: #1 total tags in treatment: 17586794 INFO @ Tue, 30 Jun 2020 01:28:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:28:02: #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 01:28:02: #1 tags after filtering in treatment: 17586794 INFO @ Tue, 30 Jun 2020 01:28:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:28:02: #1 finished! INFO @ Tue, 30 Jun 2020 01:28:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:28:04: #2 number of paired peaks: 223 WARNING @ Tue, 30 Jun 2020 01:28:04: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Tue, 30 Jun 2020 01:28:04: start model_add_line... INFO @ Tue, 30 Jun 2020 01:28:04: start X-correlation... INFO @ Tue, 30 Jun 2020 01:28:04: end of X-cor INFO @ Tue, 30 Jun 2020 01:28:04: #2 finished! INFO @ Tue, 30 Jun 2020 01:28:04: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:28:04: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 30 Jun 2020 01:28:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.20_model.r WARNING @ Tue, 30 Jun 2020 01:28:04: #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 01:28:04: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 30 Jun 2020 01:28:04: #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 01:28:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:28:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.10_summits.bed INFO @ Tue, 30 Jun 2020 01:28:15: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:28:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494841/SRX494841.20_summits.bed INFO @ Tue, 30 Jun 2020 01:28:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling