Job ID = 6367509 SRX = SRX331265 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:21 prefetch.2.10.7: 1) Downloading 'SRR947497'... 2020-06-15T23:28:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:29:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:29:14 prefetch.2.10.7: 'SRR947497' is valid 2020-06-15T23:29:14 prefetch.2.10.7: 1) 'SRR947497' was downloaded successfully Read 6816799 spots for SRR947497/SRR947497.sra Written 6816799 spots for SRR947497/SRR947497.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: 00:01:02 6816799 reads; of these: 6816799 (100.00%) were unpaired; of these: 52296 (0.77%) aligned 0 times 5681821 (83.35%) aligned exactly 1 time 1082682 (15.88%) aligned >1 times 99.23% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 523056 / 6764503 = 0.0773 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 08:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.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 08:32:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:27: 1000000 INFO @ Tue, 16 Jun 2020 08:32:34: 2000000 INFO @ Tue, 16 Jun 2020 08:32:40: 3000000 INFO @ Tue, 16 Jun 2020 08:32:47: 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 08:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.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 08:32:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:32:53: 5000000 INFO @ Tue, 16 Jun 2020 08:32:58: 1000000 INFO @ Tue, 16 Jun 2020 08:33:01: 6000000 INFO @ Tue, 16 Jun 2020 08:33:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:02: #1 total tags in treatment: 6241447 INFO @ Tue, 16 Jun 2020 08:33:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:02: #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 08:33:02: #1 tags after filtering in treatment: 6241447 INFO @ Tue, 16 Jun 2020 08:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:03: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 08:33:03: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:03: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:33:03: #2 alternative fragment length(s) may be 3,31,522,544,550 bps INFO @ Tue, 16 Jun 2020 08:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.05_model.r WARNING @ Tue, 16 Jun 2020 08:33:03: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:03: #2 You may need to consider one of the other alternative d(s): 3,31,522,544,550 WARNING @ Tue, 16 Jun 2020 08:33:03: #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 08:33:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:05: 2000000 INFO @ Tue, 16 Jun 2020 08:33:11: 3000000 INFO @ Tue, 16 Jun 2020 08:33:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:18: 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 08:33:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.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 08:33:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (511 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:24: 5000000 INFO @ Tue, 16 Jun 2020 08:33:27: 1000000 INFO @ Tue, 16 Jun 2020 08:33:31: 6000000 INFO @ Tue, 16 Jun 2020 08:33:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:33:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:33:33: #1 total tags in treatment: 6241447 INFO @ Tue, 16 Jun 2020 08:33:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:33: #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 08:33:33: #1 tags after filtering in treatment: 6241447 INFO @ Tue, 16 Jun 2020 08:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:33: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 08:33:33: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:33: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:33:33: #2 alternative fragment length(s) may be 3,31,522,544,550 bps INFO @ Tue, 16 Jun 2020 08:33:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:33: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:33: #2 You may need to consider one of the other alternative d(s): 3,31,522,544,550 WARNING @ Tue, 16 Jun 2020 08:33:33: #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 08:33:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:34: 2000000 INFO @ Tue, 16 Jun 2020 08:33:41: 3000000 INFO @ Tue, 16 Jun 2020 08:33:45: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:47: 4000000 INFO @ Tue, 16 Jun 2020 08:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:53: 5000000 INFO @ Tue, 16 Jun 2020 08:34:00: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:34:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:34:01: #1 total tags in treatment: 6241447 INFO @ Tue, 16 Jun 2020 08:34:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:01: #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 08:34:01: #1 tags after filtering in treatment: 6241447 INFO @ Tue, 16 Jun 2020 08:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:02: #2 number of paired peaks: 419 WARNING @ Tue, 16 Jun 2020 08:34:02: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:02: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:34:02: #2 alternative fragment length(s) may be 3,31,522,544,550 bps INFO @ Tue, 16 Jun 2020 08:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.20_model.r WARNING @ Tue, 16 Jun 2020 08:34:02: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:34:02: #2 You may need to consider one of the other alternative d(s): 3,31,522,544,550 WARNING @ Tue, 16 Jun 2020 08:34:02: #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 08:34:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331265/SRX331265.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis CompletedMACS2peakCalling