Job ID = 6458009 SRX = SRX4933911 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:14:37 prefetch.2.10.7: 1) Downloading 'SRR8107302'... 2020-06-21T12:14:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:16:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:16:35 prefetch.2.10.7: 'SRR8107302' is valid 2020-06-21T12:16:35 prefetch.2.10.7: 1) 'SRR8107302' was downloaded successfully Read 15321809 spots for SRR8107302/SRR8107302.sra Written 15321809 spots for SRR8107302/SRR8107302.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: 00:04:33 15321809 reads; of these: 15321809 (100.00%) were unpaired; of these: 456248 (2.98%) aligned 0 times 10617936 (69.30%) aligned exactly 1 time 4247625 (27.72%) aligned >1 times 97.02% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2282309 / 14865561 = 0.1535 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 @ Sun, 21 Jun 2020 21:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:26:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:15: 1000000 INFO @ Sun, 21 Jun 2020 21:26:20: 2000000 INFO @ Sun, 21 Jun 2020 21:26:26: 3000000 INFO @ Sun, 21 Jun 2020 21:26:31: 4000000 INFO @ Sun, 21 Jun 2020 21:26:36: 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 @ Sun, 21 Jun 2020 21:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:26:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:41: 6000000 INFO @ Sun, 21 Jun 2020 21:26:46: 1000000 INFO @ Sun, 21 Jun 2020 21:26:47: 7000000 INFO @ Sun, 21 Jun 2020 21:26:51: 2000000 INFO @ Sun, 21 Jun 2020 21:26:53: 8000000 INFO @ Sun, 21 Jun 2020 21:26:57: 3000000 INFO @ Sun, 21 Jun 2020 21:26:59: 9000000 INFO @ Sun, 21 Jun 2020 21:27:03: 4000000 INFO @ Sun, 21 Jun 2020 21:27:05: 10000000 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 @ Sun, 21 Jun 2020 21:27:08: 5000000 INFO @ Sun, 21 Jun 2020 21:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 21:27:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:11: 11000000 INFO @ Sun, 21 Jun 2020 21:27:14: 6000000 INFO @ Sun, 21 Jun 2020 21:27:16: 1000000 INFO @ Sun, 21 Jun 2020 21:27:16: 12000000 INFO @ Sun, 21 Jun 2020 21:27:20: 7000000 INFO @ Sun, 21 Jun 2020 21:27:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:27:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:27:20: #1 total tags in treatment: 12583252 INFO @ Sun, 21 Jun 2020 21:27:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:27:21: #1 tags after filtering in treatment: 12583249 INFO @ Sun, 21 Jun 2020 21:27:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:21: 2000000 INFO @ Sun, 21 Jun 2020 21:27:22: #2 number of paired peaks: 571 WARNING @ Sun, 21 Jun 2020 21:27:22: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 21 Jun 2020 21:27:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:22: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:27:22: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 21:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.05_model.r WARNING @ Sun, 21 Jun 2020 21:27:22: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:27:22: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 21:27:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:27:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:26: 8000000 INFO @ Sun, 21 Jun 2020 21:27:27: 3000000 INFO @ Sun, 21 Jun 2020 21:27:31: 9000000 INFO @ Sun, 21 Jun 2020 21:27:33: 4000000 INFO @ Sun, 21 Jun 2020 21:27:37: 10000000 INFO @ Sun, 21 Jun 2020 21:27:38: 5000000 INFO @ Sun, 21 Jun 2020 21:27:43: 11000000 INFO @ Sun, 21 Jun 2020 21:27:44: 6000000 INFO @ Sun, 21 Jun 2020 21:27:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:27:49: 12000000 INFO @ Sun, 21 Jun 2020 21:27:50: 7000000 INFO @ Sun, 21 Jun 2020 21:27:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:27:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:27:52: #1 total tags in treatment: 12583252 INFO @ Sun, 21 Jun 2020 21:27:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:27:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:27:53: #1 tags after filtering in treatment: 12583249 INFO @ Sun, 21 Jun 2020 21:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:27:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:27:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:27:54: #2 number of paired peaks: 571 WARNING @ Sun, 21 Jun 2020 21:27:54: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 21 Jun 2020 21:27:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:27:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:27:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:27:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:27:54: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:27:54: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 21:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.10_model.r WARNING @ Sun, 21 Jun 2020 21:27:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:27:54: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 21:27:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:27:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:27:55: 8000000 INFO @ Sun, 21 Jun 2020 21:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.05_summits.bed INFO @ Sun, 21 Jun 2020 21:27:57: Done! pass1 - making usageList (647 chroms): 2 millis pass2 - checking and writing primary data (2517 records, 4 fields): 95 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:28:00: 9000000 INFO @ Sun, 21 Jun 2020 21:28:06: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:28:11: 11000000 INFO @ Sun, 21 Jun 2020 21:28:16: 12000000 INFO @ Sun, 21 Jun 2020 21:28:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:28:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:28:19: #1 total tags in treatment: 12583252 INFO @ Sun, 21 Jun 2020 21:28:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:28:20: #1 tags after filtering in treatment: 12583249 INFO @ Sun, 21 Jun 2020 21:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:21: #2 number of paired peaks: 571 WARNING @ Sun, 21 Jun 2020 21:28:21: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 21 Jun 2020 21:28:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:21: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:28:21: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 21:28:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.20_model.r WARNING @ Sun, 21 Jun 2020 21:28:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:21: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 21:28:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:28:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.10_summits.bed INFO @ Sun, 21 Jun 2020 21:28:29: Done! pass1 - making usageList (541 chroms): 1 millis pass2 - checking and writing primary data (1846 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:28:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:28:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:28:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:28:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933911/SRX4933911.20_summits.bed INFO @ Sun, 21 Jun 2020 21:28:57: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 8 millis CompletedMACS2peakCalling