Job ID = 6367478 SRX = SRX331235 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:25:51 prefetch.2.10.7: 1) Downloading 'SRR947467'... 2020-06-15T23:25:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:26:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:26:33 prefetch.2.10.7: 'SRR947467' is valid 2020-06-15T23:26:33 prefetch.2.10.7: 1) 'SRR947467' was downloaded successfully Read 7853525 spots for SRR947467/SRR947467.sra Written 7853525 spots for SRR947467/SRR947467.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: 00:01:15 7853525 reads; of these: 7853525 (100.00%) were unpaired; of these: 154195 (1.96%) aligned 0 times 6219618 (79.20%) aligned exactly 1 time 1479712 (18.84%) aligned >1 times 98.04% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 1122078 / 7699330 = 0.1457 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 08:30:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.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 08:30:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:39: 1000000 INFO @ Tue, 16 Jun 2020 08:30:44: 2000000 INFO @ Tue, 16 Jun 2020 08:30:48: 3000000 INFO @ Tue, 16 Jun 2020 08:30:53: 4000000 INFO @ Tue, 16 Jun 2020 08:30:58: 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 08:31:02: 6000000 INFO @ Tue, 16 Jun 2020 08:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.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 08:31:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:05: #1 total tags in treatment: 6577252 INFO @ Tue, 16 Jun 2020 08:31:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:05: #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 08:31:05: #1 tags after filtering in treatment: 6577252 INFO @ Tue, 16 Jun 2020 08:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:05: #2 number of paired peaks: 507 WARNING @ Tue, 16 Jun 2020 08:31:05: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:06: #2 predicted fragment length is 26 bps INFO @ Tue, 16 Jun 2020 08:31:06: #2 alternative fragment length(s) may be 2,26,507,513 bps INFO @ Tue, 16 Jun 2020 08:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.05_model.r WARNING @ Tue, 16 Jun 2020 08:31:06: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:06: #2 You may need to consider one of the other alternative d(s): 2,26,507,513 WARNING @ Tue, 16 Jun 2020 08:31:06: #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 08:31:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:08: 1000000 INFO @ Tue, 16 Jun 2020 08:31:13: 2000000 INFO @ Tue, 16 Jun 2020 08:31:17: 3000000 INFO @ Tue, 16 Jun 2020 08:31:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:22: 4000000 INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.05_summits.bed INFO @ Tue, 16 Jun 2020 08:31:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:26: 5000000 INFO @ Tue, 16 Jun 2020 08:31:31: 6000000 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 08:31:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:33: #1 total tags in treatment: 6577252 INFO @ Tue, 16 Jun 2020 08:31:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:33: #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 08:31:34: #1 tags after filtering in treatment: 6577252 INFO @ Tue, 16 Jun 2020 08:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.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 08:31:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:34: #2 number of paired peaks: 507 WARNING @ Tue, 16 Jun 2020 08:31:34: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:34: #2 predicted fragment length is 26 bps INFO @ Tue, 16 Jun 2020 08:31:34: #2 alternative fragment length(s) may be 2,26,507,513 bps INFO @ Tue, 16 Jun 2020 08:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.10_model.r WARNING @ Tue, 16 Jun 2020 08:31:34: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:34: #2 You may need to consider one of the other alternative d(s): 2,26,507,513 WARNING @ Tue, 16 Jun 2020 08:31:34: #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 08:31:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:31:38: 1000000 INFO @ Tue, 16 Jun 2020 08:31:43: 2000000 INFO @ Tue, 16 Jun 2020 08:31:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:47: 3000000 INFO @ Tue, 16 Jun 2020 08:31:52: 4000000 INFO @ Tue, 16 Jun 2020 08:31:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:56: 5000000 INFO @ Tue, 16 Jun 2020 08:32:01: 6000000 INFO @ Tue, 16 Jun 2020 08:32:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:32:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:32:04: #1 total tags in treatment: 6577252 INFO @ Tue, 16 Jun 2020 08:32:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:04: #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 08:32:04: #1 tags after filtering in treatment: 6577252 INFO @ Tue, 16 Jun 2020 08:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:04: #2 number of paired peaks: 507 WARNING @ Tue, 16 Jun 2020 08:32:04: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:04: #2 predicted fragment length is 26 bps INFO @ Tue, 16 Jun 2020 08:32:04: #2 alternative fragment length(s) may be 2,26,507,513 bps INFO @ Tue, 16 Jun 2020 08:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.20_model.r WARNING @ Tue, 16 Jun 2020 08:32:04: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:04: #2 You may need to consider one of the other alternative d(s): 2,26,507,513 WARNING @ Tue, 16 Jun 2020 08:32:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:32:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331235/SRX331235.20_summits.bed INFO @ Tue, 16 Jun 2020 08:32:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。