Job ID = 6366788 SRX = SRX233453 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:03:08 prefetch.2.10.7: 1) Downloading 'SRR701509'... 2020-06-15T23:03:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:38 prefetch.2.10.7: 'SRR701509' is valid 2020-06-15T23:03:38 prefetch.2.10.7: 1) 'SRR701509' was downloaded successfully Read 7931160 spots for SRR701509/SRR701509.sra Written 7931160 spots for SRR701509/SRR701509.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: 00:00:50 7931160 reads; of these: 7931160 (100.00%) were unpaired; of these: 4213598 (53.13%) aligned 0 times 3054019 (38.51%) aligned exactly 1 time 663543 (8.37%) aligned >1 times 46.87% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 200605 / 3717562 = 0.0540 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 08:06:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.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 08:06:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:08: 1000000 INFO @ Tue, 16 Jun 2020 08:06:13: 2000000 INFO @ Tue, 16 Jun 2020 08:06:17: 3000000 INFO @ Tue, 16 Jun 2020 08:06:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:06:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:06:19: #1 total tags in treatment: 3516957 INFO @ Tue, 16 Jun 2020 08:06:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:19: #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 08:06:19: #1 tags after filtering in treatment: 3516957 INFO @ Tue, 16 Jun 2020 08:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:20: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:06:20: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:20: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:06:20: #2 alternative fragment length(s) may be 42,87 bps INFO @ Tue, 16 Jun 2020 08:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:20: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:20: #2 You may need to consider one of the other alternative d(s): 42,87 WARNING @ Tue, 16 Jun 2020 08:06:20: #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 08:06:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (839 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.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 08:06:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:39: 1000000 INFO @ Tue, 16 Jun 2020 08:06:44: 2000000 INFO @ Tue, 16 Jun 2020 08:06:49: 3000000 INFO @ Tue, 16 Jun 2020 08:06:51: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:06:51: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:06:51: #1 total tags in treatment: 3516957 INFO @ Tue, 16 Jun 2020 08:06:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:51: #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 08:06:51: #1 tags after filtering in treatment: 3516957 INFO @ Tue, 16 Jun 2020 08:06:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:52: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:06:52: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:52: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:06:52: #2 alternative fragment length(s) may be 42,87 bps INFO @ Tue, 16 Jun 2020 08:06:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:52: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:52: #2 You may need to consider one of the other alternative d(s): 42,87 WARNING @ Tue, 16 Jun 2020 08:06:52: #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 08:06:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:59: #3 Call peaks for each chromosome... 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 08:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.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 08:07:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:09: 1000000 INFO @ Tue, 16 Jun 2020 08:07:13: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:18: 3000000 INFO @ Tue, 16 Jun 2020 08:07:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:07:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:07:20: #1 total tags in treatment: 3516957 INFO @ Tue, 16 Jun 2020 08:07:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:20: #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 08:07:20: #1 tags after filtering in treatment: 3516957 INFO @ Tue, 16 Jun 2020 08:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:21: #2 number of paired peaks: 429 WARNING @ Tue, 16 Jun 2020 08:07:21: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:21: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:07:21: #2 alternative fragment length(s) may be 42,87 bps INFO @ Tue, 16 Jun 2020 08:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:21: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:21: #2 You may need to consider one of the other alternative d(s): 42,87 WARNING @ Tue, 16 Jun 2020 08:07:21: #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 08:07:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233453/SRX233453.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 1 millis CompletedMACS2peakCalling