Job ID = 6366761 SRX = SRX2228914 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:38 prefetch.2.10.7: 1) Downloading 'SRR4380370'... 2020-06-15T22:59:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:27 prefetch.2.10.7: 'SRR4380370' is valid 2020-06-15T23:00:27 prefetch.2.10.7: 1) 'SRR4380370' was downloaded successfully Read 10075319 spots for SRR4380370/SRR4380370.sra Written 10075319 spots for SRR4380370/SRR4380370.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: 00:01:46 10075319 reads; of these: 10075319 (100.00%) were unpaired; of these: 1467993 (14.57%) aligned 0 times 6959196 (69.07%) aligned exactly 1 time 1648130 (16.36%) aligned >1 times 85.43% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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_rmdupse_core] 1384660 / 8607326 = 0.1609 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 08:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.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 08:05:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:18: 1000000 INFO @ Tue, 16 Jun 2020 08:05:24: 2000000 INFO @ Tue, 16 Jun 2020 08:05:31: 3000000 INFO @ Tue, 16 Jun 2020 08:05:37: 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 08:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.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 08:05:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:44: 5000000 INFO @ Tue, 16 Jun 2020 08:05:48: 1000000 INFO @ Tue, 16 Jun 2020 08:05:52: 6000000 INFO @ Tue, 16 Jun 2020 08:05:56: 2000000 INFO @ Tue, 16 Jun 2020 08:05:59: 7000000 INFO @ Tue, 16 Jun 2020 08:06:01: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:06:01: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:06:01: #1 total tags in treatment: 7222666 INFO @ Tue, 16 Jun 2020 08:06:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:01: #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 08:06:01: #1 tags after filtering in treatment: 7222666 INFO @ Tue, 16 Jun 2020 08:06:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:01: #2 number of paired peaks: 550 WARNING @ Tue, 16 Jun 2020 08:06:01: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:02: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 08:06:02: #2 alternative fragment length(s) may be 4,63,74 bps INFO @ Tue, 16 Jun 2020 08:06:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:02: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:02: #2 You may need to consider one of the other alternative d(s): 4,63,74 WARNING @ Tue, 16 Jun 2020 08:06:02: #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 08:06:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:02: 3000000 INFO @ Tue, 16 Jun 2020 08:06:09: 4000000 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 08:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.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 08:06:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:16: 5000000 INFO @ Tue, 16 Jun 2020 08:06:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:18: 1000000 INFO @ Tue, 16 Jun 2020 08:06:22: 6000000 INFO @ Tue, 16 Jun 2020 08:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2123 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:25: 2000000 INFO @ Tue, 16 Jun 2020 08:06:29: 7000000 INFO @ Tue, 16 Jun 2020 08:06:31: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:06:31: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:06:31: #1 total tags in treatment: 7222666 INFO @ Tue, 16 Jun 2020 08:06:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:31: #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 08:06:31: #1 tags after filtering in treatment: 7222666 INFO @ Tue, 16 Jun 2020 08:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:31: #2 number of paired peaks: 550 WARNING @ Tue, 16 Jun 2020 08:06:31: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:31: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 08:06:31: #2 alternative fragment length(s) may be 4,63,74 bps INFO @ Tue, 16 Jun 2020 08:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:31: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:31: #2 You may need to consider one of the other alternative d(s): 4,63,74 WARNING @ Tue, 16 Jun 2020 08:06:31: #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 08:06:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:32: 3000000 INFO @ Tue, 16 Jun 2020 08:06:38: 4000000 INFO @ Tue, 16 Jun 2020 08:06:44: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:50: 6000000 INFO @ Tue, 16 Jun 2020 08:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:56: 7000000 INFO @ Tue, 16 Jun 2020 08:06:57: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:06:57: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:06:57: #1 total tags in treatment: 7222666 INFO @ Tue, 16 Jun 2020 08:06:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:57: #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 08:06:57: #1 tags after filtering in treatment: 7222666 INFO @ Tue, 16 Jun 2020 08:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:58: #2 number of paired peaks: 550 WARNING @ Tue, 16 Jun 2020 08:06:58: Fewer paired peaks (550) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 550 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:58: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2 alternative fragment length(s) may be 4,63,74 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:58: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:58: #2 You may need to consider one of the other alternative d(s): 4,63,74 WARNING @ Tue, 16 Jun 2020 08:06:58: #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 08:06:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228914/SRX2228914.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling