Job ID = 6366078 SRX = SRX059250 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:29 prefetch.2.10.7: 1) Downloading 'SRR190690'... 2020-06-15T22:29:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:52 prefetch.2.10.7: 'SRR190690' is valid 2020-06-15T22:30:52 prefetch.2.10.7: 1) 'SRR190690' was downloaded successfully Read 16864948 spots for SRR190690/SRR190690.sra Written 16864948 spots for SRR190690/SRR190690.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: 00:03:01 16864948 reads; of these: 16864948 (100.00%) were unpaired; of these: 917351 (5.44%) aligned 0 times 13167345 (78.08%) aligned exactly 1 time 2780252 (16.49%) aligned >1 times 94.56% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 2595786 / 15947597 = 0.1628 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 07:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.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 07:39:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:07: 1000000 INFO @ Tue, 16 Jun 2020 07:39:13: 2000000 INFO @ Tue, 16 Jun 2020 07:39:20: 3000000 INFO @ Tue, 16 Jun 2020 07:39:26: 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 07:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.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 07:39:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:32: 5000000 INFO @ Tue, 16 Jun 2020 07:39:38: 1000000 INFO @ Tue, 16 Jun 2020 07:39:38: 6000000 INFO @ Tue, 16 Jun 2020 07:39:44: 2000000 INFO @ Tue, 16 Jun 2020 07:39:45: 7000000 INFO @ Tue, 16 Jun 2020 07:39:51: 3000000 INFO @ Tue, 16 Jun 2020 07:39:51: 8000000 INFO @ Tue, 16 Jun 2020 07:39:57: 4000000 INFO @ Tue, 16 Jun 2020 07:39:58: 9000000 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 07:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.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 07:40:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:04: 5000000 INFO @ Tue, 16 Jun 2020 07:40:04: 10000000 INFO @ Tue, 16 Jun 2020 07:40:08: 1000000 INFO @ Tue, 16 Jun 2020 07:40:10: 6000000 INFO @ Tue, 16 Jun 2020 07:40:11: 11000000 INFO @ Tue, 16 Jun 2020 07:40:14: 2000000 INFO @ Tue, 16 Jun 2020 07:40:17: 7000000 INFO @ Tue, 16 Jun 2020 07:40:17: 12000000 INFO @ Tue, 16 Jun 2020 07:40:20: 3000000 INFO @ Tue, 16 Jun 2020 07:40:24: 13000000 INFO @ Tue, 16 Jun 2020 07:40:24: 8000000 INFO @ Tue, 16 Jun 2020 07:40:26: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:40:26: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:40:26: #1 total tags in treatment: 13351811 INFO @ Tue, 16 Jun 2020 07:40:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:26: #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 07:40:26: 4000000 INFO @ Tue, 16 Jun 2020 07:40:26: #1 tags after filtering in treatment: 13351811 INFO @ Tue, 16 Jun 2020 07:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:27: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 07:40:27: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:27: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:27: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:27: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:27: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:27: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:40:27: #2 alternative fragment length(s) may be 3,47,59,61,567 bps INFO @ Tue, 16 Jun 2020 07:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.05_model.r WARNING @ Tue, 16 Jun 2020 07:40:27: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:40:27: #2 You may need to consider one of the other alternative d(s): 3,47,59,61,567 WARNING @ Tue, 16 Jun 2020 07:40:27: #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 07:40:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:40:30: 9000000 INFO @ Tue, 16 Jun 2020 07:40:32: 5000000 INFO @ Tue, 16 Jun 2020 07:40:37: 10000000 INFO @ Tue, 16 Jun 2020 07:40:38: 6000000 INFO @ Tue, 16 Jun 2020 07:40:43: 11000000 INFO @ Tue, 16 Jun 2020 07:40:45: 7000000 INFO @ Tue, 16 Jun 2020 07:40:49: 12000000 INFO @ Tue, 16 Jun 2020 07:40:51: 8000000 INFO @ Tue, 16 Jun 2020 07:40:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:55: 13000000 INFO @ Tue, 16 Jun 2020 07:40:57: 9000000 INFO @ Tue, 16 Jun 2020 07:40:58: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:40:58: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:40:58: #1 total tags in treatment: 13351811 INFO @ Tue, 16 Jun 2020 07:40:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:58: #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 07:40:58: #1 tags after filtering in treatment: 13351811 INFO @ Tue, 16 Jun 2020 07:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:59: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 07:40:59: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 07:40:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:59: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:40:59: #2 alternative fragment length(s) may be 3,47,59,61,567 bps INFO @ Tue, 16 Jun 2020 07:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.10_model.r WARNING @ Tue, 16 Jun 2020 07:40:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:40:59: #2 You may need to consider one of the other alternative d(s): 3,47,59,61,567 WARNING @ Tue, 16 Jun 2020 07:40:59: #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 07:40:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:03: 10000000 INFO @ Tue, 16 Jun 2020 07:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2467 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:41:09: 11000000 INFO @ Tue, 16 Jun 2020 07:41:14: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:41:20: 13000000 INFO @ Tue, 16 Jun 2020 07:41:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:41:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:41:22: #1 total tags in treatment: 13351811 INFO @ Tue, 16 Jun 2020 07:41:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:22: #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 07:41:22: #1 tags after filtering in treatment: 13351811 INFO @ Tue, 16 Jun 2020 07:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:23: #2 number of paired peaks: 231 WARNING @ Tue, 16 Jun 2020 07:41:23: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 16 Jun 2020 07:41:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:23: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 07:41:23: #2 alternative fragment length(s) may be 3,47,59,61,567 bps INFO @ Tue, 16 Jun 2020 07:41:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.20_model.r WARNING @ Tue, 16 Jun 2020 07:41:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:41:23: #2 You may need to consider one of the other alternative d(s): 3,47,59,61,567 WARNING @ Tue, 16 Jun 2020 07:41:23: #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 07:41:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.10_summits.bed INFO @ Tue, 16 Jun 2020 07:41:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1328 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:41:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059250/SRX059250.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (569 records, 4 fields): 2 millis CompletedMACS2peakCalling