Job ID = 6368745 SRX = SRX5402768 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:57 prefetch.2.10.7: 1) Downloading 'SRR8603002'... 2020-06-16T00:30:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:45 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:45 prefetch.2.10.7: 1) 'SRR8603002' was downloaded successfully Read 36340592 spots for SRR8603002/SRR8603002.sra Written 36340592 spots for SRR8603002/SRR8603002.sra 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: 00:05:59 36340592 reads; of these: 36340592 (100.00%) were unpaired; of these: 16638007 (45.78%) aligned 0 times 16273557 (44.78%) aligned exactly 1 time 3429028 (9.44%) aligned >1 times 54.22% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 2181765 / 19702585 = 0.1107 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, 16 Jun 2020 09:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.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, 16 Jun 2020 09:50:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:23: 1000000 INFO @ Tue, 16 Jun 2020 09:50:29: 2000000 INFO @ Tue, 16 Jun 2020 09:50:35: 3000000 INFO @ Tue, 16 Jun 2020 09:50:41: 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 @ Tue, 16 Jun 2020 09:50:47: 5000000 INFO @ Tue, 16 Jun 2020 09:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.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, 16 Jun 2020 09:50:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:54: 6000000 INFO @ Tue, 16 Jun 2020 09:50:54: 1000000 INFO @ Tue, 16 Jun 2020 09:51:01: 7000000 INFO @ Tue, 16 Jun 2020 09:51:02: 2000000 INFO @ Tue, 16 Jun 2020 09:51:08: 8000000 INFO @ Tue, 16 Jun 2020 09:51:09: 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, 16 Jun 2020 09:51:16: 9000000 INFO @ Tue, 16 Jun 2020 09:51:17: 4000000 INFO @ Tue, 16 Jun 2020 09:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.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, 16 Jun 2020 09:51:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:23: 10000000 INFO @ Tue, 16 Jun 2020 09:51:24: 5000000 INFO @ Tue, 16 Jun 2020 09:51:25: 1000000 INFO @ Tue, 16 Jun 2020 09:51:31: 11000000 INFO @ Tue, 16 Jun 2020 09:51:32: 6000000 INFO @ Tue, 16 Jun 2020 09:51:33: 2000000 INFO @ Tue, 16 Jun 2020 09:51:39: 12000000 INFO @ Tue, 16 Jun 2020 09:51:40: 7000000 INFO @ Tue, 16 Jun 2020 09:51:42: 3000000 INFO @ Tue, 16 Jun 2020 09:51:46: 13000000 INFO @ Tue, 16 Jun 2020 09:51:47: 8000000 INFO @ Tue, 16 Jun 2020 09:51:50: 4000000 INFO @ Tue, 16 Jun 2020 09:51:54: 14000000 INFO @ Tue, 16 Jun 2020 09:51:55: 9000000 INFO @ Tue, 16 Jun 2020 09:51:58: 5000000 INFO @ Tue, 16 Jun 2020 09:52:01: 15000000 INFO @ Tue, 16 Jun 2020 09:52:03: 10000000 INFO @ Tue, 16 Jun 2020 09:52:07: 6000000 INFO @ Tue, 16 Jun 2020 09:52:09: 16000000 INFO @ Tue, 16 Jun 2020 09:52:11: 11000000 INFO @ Tue, 16 Jun 2020 09:52:15: 7000000 INFO @ Tue, 16 Jun 2020 09:52:16: 17000000 INFO @ Tue, 16 Jun 2020 09:52:18: 12000000 INFO @ Tue, 16 Jun 2020 09:52:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:52:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:52:20: #1 total tags in treatment: 17520820 INFO @ Tue, 16 Jun 2020 09:52:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:52:20: #1 tags after filtering in treatment: 17520820 INFO @ Tue, 16 Jun 2020 09:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:21: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:52:21: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:52:22: #2 alternative fragment length(s) may be 1,42,563 bps INFO @ Tue, 16 Jun 2020 09:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:22: #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, 16 Jun 2020 09:52:22: #2 You may need to consider one of the other alternative d(s): 1,42,563 WARNING @ Tue, 16 Jun 2020 09:52:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:52:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:24: 8000000 INFO @ Tue, 16 Jun 2020 09:52:26: 13000000 INFO @ Tue, 16 Jun 2020 09:52:32: 9000000 INFO @ Tue, 16 Jun 2020 09:52:33: 14000000 INFO @ Tue, 16 Jun 2020 09:52:41: 10000000 INFO @ Tue, 16 Jun 2020 09:52:41: 15000000 INFO @ Tue, 16 Jun 2020 09:52:49: 16000000 INFO @ Tue, 16 Jun 2020 09:52:49: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:52:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:56: 17000000 INFO @ Tue, 16 Jun 2020 09:52:58: 12000000 INFO @ Tue, 16 Jun 2020 09:53:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:00: #1 total tags in treatment: 17520820 INFO @ Tue, 16 Jun 2020 09:53:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:53:01: #1 tags after filtering in treatment: 17520820 INFO @ Tue, 16 Jun 2020 09:53:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:02: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:53:02: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:53:02: #2 alternative fragment length(s) may be 1,42,563 bps INFO @ Tue, 16 Jun 2020 09:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.10_model.r WARNING @ Tue, 16 Jun 2020 09:53:02: #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, 16 Jun 2020 09:53:02: #2 You may need to consider one of the other alternative d(s): 1,42,563 WARNING @ Tue, 16 Jun 2020 09:53:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:53:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:06: 13000000 INFO @ Tue, 16 Jun 2020 09:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:14: 14000000 INFO @ Tue, 16 Jun 2020 09:53:23: 15000000 INFO @ Tue, 16 Jun 2020 09:53:31: 16000000 INFO @ Tue, 16 Jun 2020 09:53:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:53:38: 17000000 INFO @ Tue, 16 Jun 2020 09:53:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:53:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:53:42: #1 total tags in treatment: 17520820 INFO @ Tue, 16 Jun 2020 09:53:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:53:43: #1 tags after filtering in treatment: 17520820 INFO @ Tue, 16 Jun 2020 09:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:44: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:53:44: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:44: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:53:44: #2 alternative fragment length(s) may be 1,42,563 bps INFO @ Tue, 16 Jun 2020 09:53:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.20_model.r WARNING @ Tue, 16 Jun 2020 09:53:44: #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, 16 Jun 2020 09:53:44: #2 You may need to consider one of the other alternative d(s): 1,42,563 WARNING @ Tue, 16 Jun 2020 09:53:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:53:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402768/SRX5402768.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling