Job ID = 6365818 SRX = ERX1270342 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:11:42 prefetch.2.10.7: 1) Downloading 'ERR1198083'... 2020-06-15T22:11:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:13:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:13:20 prefetch.2.10.7: 'ERR1198083' is valid 2020-06-15T22:13:20 prefetch.2.10.7: 1) 'ERR1198083' was downloaded successfully Read 21538826 spots for ERR1198083/ERR1198083.sra Written 21538826 spots for ERR1198083/ERR1198083.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:54 21538826 reads; of these: 21538826 (100.00%) were unpaired; of these: 287717 (1.34%) aligned 0 times 17833377 (82.80%) aligned exactly 1 time 3417732 (15.87%) aligned >1 times 98.66% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 1893513 / 21251109 = 0.0891 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 07:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.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 07:25:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:05: 1000000 INFO @ Tue, 16 Jun 2020 07:25:11: 2000000 INFO @ Tue, 16 Jun 2020 07:25:16: 3000000 INFO @ Tue, 16 Jun 2020 07:25:21: 4000000 INFO @ Tue, 16 Jun 2020 07:25:27: 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, 16 Jun 2020 07:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.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 07:25:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:32: 6000000 INFO @ Tue, 16 Jun 2020 07:25:36: 1000000 INFO @ Tue, 16 Jun 2020 07:25:38: 7000000 INFO @ Tue, 16 Jun 2020 07:25:42: 2000000 INFO @ Tue, 16 Jun 2020 07:25:43: 8000000 INFO @ Tue, 16 Jun 2020 07:25:48: 3000000 INFO @ Tue, 16 Jun 2020 07:25:49: 9000000 INFO @ Tue, 16 Jun 2020 07:25:54: 4000000 INFO @ Tue, 16 Jun 2020 07:25:55: 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, 16 Jun 2020 07:26:00: 5000000 INFO @ Tue, 16 Jun 2020 07:26:00: 11000000 INFO @ Tue, 16 Jun 2020 07:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.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 07:26:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:06: 6000000 INFO @ Tue, 16 Jun 2020 07:26:06: 12000000 INFO @ Tue, 16 Jun 2020 07:26:06: 1000000 INFO @ Tue, 16 Jun 2020 07:26:11: 7000000 INFO @ Tue, 16 Jun 2020 07:26:12: 13000000 INFO @ Tue, 16 Jun 2020 07:26:12: 2000000 INFO @ Tue, 16 Jun 2020 07:26:17: 8000000 INFO @ Tue, 16 Jun 2020 07:26:17: 14000000 INFO @ Tue, 16 Jun 2020 07:26:18: 3000000 INFO @ Tue, 16 Jun 2020 07:26:23: 15000000 INFO @ Tue, 16 Jun 2020 07:26:23: 9000000 INFO @ Tue, 16 Jun 2020 07:26:23: 4000000 INFO @ Tue, 16 Jun 2020 07:26:29: 16000000 INFO @ Tue, 16 Jun 2020 07:26:29: 10000000 INFO @ Tue, 16 Jun 2020 07:26:29: 5000000 INFO @ Tue, 16 Jun 2020 07:26:34: 17000000 INFO @ Tue, 16 Jun 2020 07:26:35: 11000000 INFO @ Tue, 16 Jun 2020 07:26:35: 6000000 INFO @ Tue, 16 Jun 2020 07:26:40: 18000000 INFO @ Tue, 16 Jun 2020 07:26:40: 12000000 INFO @ Tue, 16 Jun 2020 07:26:41: 7000000 INFO @ Tue, 16 Jun 2020 07:26:46: 19000000 INFO @ Tue, 16 Jun 2020 07:26:46: 13000000 INFO @ Tue, 16 Jun 2020 07:26:46: 8000000 INFO @ Tue, 16 Jun 2020 07:26:48: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:26:48: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:26:48: #1 total tags in treatment: 19357596 INFO @ Tue, 16 Jun 2020 07:26:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:48: #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 07:26:48: #1 tags after filtering in treatment: 19357596 INFO @ Tue, 16 Jun 2020 07:26:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:48: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:50: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 07:26:50: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 07:26:50: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:50: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:50: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:50: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:50: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:26:50: #2 alternative fragment length(s) may be 1,46,548,574 bps INFO @ Tue, 16 Jun 2020 07:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.05_model.r WARNING @ Tue, 16 Jun 2020 07:26:50: #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 07:26:50: #2 You may need to consider one of the other alternative d(s): 1,46,548,574 WARNING @ Tue, 16 Jun 2020 07:26:50: #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 07:26:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:26:52: 14000000 INFO @ Tue, 16 Jun 2020 07:26:52: 9000000 INFO @ Tue, 16 Jun 2020 07:26:58: 15000000 INFO @ Tue, 16 Jun 2020 07:26:58: 10000000 INFO @ Tue, 16 Jun 2020 07:27:03: 16000000 INFO @ Tue, 16 Jun 2020 07:27:04: 11000000 INFO @ Tue, 16 Jun 2020 07:27:09: 17000000 INFO @ Tue, 16 Jun 2020 07:27:09: 12000000 INFO @ Tue, 16 Jun 2020 07:27:15: 13000000 INFO @ Tue, 16 Jun 2020 07:27:15: 18000000 INFO @ Tue, 16 Jun 2020 07:27:21: 14000000 INFO @ Tue, 16 Jun 2020 07:27:21: 19000000 INFO @ Tue, 16 Jun 2020 07:27:23: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:27:23: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:27:23: #1 total tags in treatment: 19357596 INFO @ Tue, 16 Jun 2020 07:27:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:23: #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 07:27:24: #1 tags after filtering in treatment: 19357596 INFO @ Tue, 16 Jun 2020 07:27:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:24: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:27:25: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 07:27:25: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:25: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:25: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:25: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:25: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:27:25: #2 alternative fragment length(s) may be 1,46,548,574 bps INFO @ Tue, 16 Jun 2020 07:27:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.10_model.r WARNING @ Tue, 16 Jun 2020 07:27:25: #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 07:27:25: #2 You may need to consider one of the other alternative d(s): 1,46,548,574 WARNING @ Tue, 16 Jun 2020 07:27:25: #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 07:27:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:27:26: 15000000 INFO @ Tue, 16 Jun 2020 07:27:32: 16000000 INFO @ Tue, 16 Jun 2020 07:27:37: 17000000 INFO @ Tue, 16 Jun 2020 07:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.05_summits.bed INFO @ Tue, 16 Jun 2020 07:27:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:27:42: 18000000 INFO @ Tue, 16 Jun 2020 07:27:48: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:27:50: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 07:27:50: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 07:27:50: #1 total tags in treatment: 19357596 INFO @ Tue, 16 Jun 2020 07:27:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:27:50: #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 07:27:50: #1 tags after filtering in treatment: 19357596 INFO @ Tue, 16 Jun 2020 07:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:27:50: #1 finished! INFO @ Tue, 16 Jun 2020 07:27:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:27:51: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 07:27:51: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 07:27:51: start model_add_line... INFO @ Tue, 16 Jun 2020 07:27:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:27:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:27:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:27:52: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:27:52: #2 alternative fragment length(s) may be 1,46,548,574 bps INFO @ Tue, 16 Jun 2020 07:27:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.20_model.r WARNING @ Tue, 16 Jun 2020 07:27:52: #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 07:27:52: #2 You may need to consider one of the other alternative d(s): 1,46,548,574 WARNING @ Tue, 16 Jun 2020 07:27:52: #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 07:27:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:27:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:28:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.10_summits.bed INFO @ Tue, 16 Jun 2020 07:28:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:28:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1270342/ERX1270342.20_summits.bed INFO @ Tue, 16 Jun 2020 07:28:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling