Job ID = 6458330 SRX = SRX5011077 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:07 prefetch.2.10.7: 1) Downloading 'SRR8191526'... 2020-06-21T12:20:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:25:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:25:53 prefetch.2.10.7: 1) 'SRR8191526' was downloaded successfully Read 48617397 spots for SRR8191526/SRR8191526.sra Written 48617397 spots for SRR8191526/SRR8191526.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: 00:11:55 48617397 reads; of these: 48617397 (100.00%) were unpaired; of these: 8228582 (16.93%) aligned 0 times 30460093 (62.65%) aligned exactly 1 time 9928722 (20.42%) aligned >1 times 83.07% overall alignment rate Time searching: 00:11:55 Overall time: 00:11:55 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 20 files... [bam_rmdupse_core] 16946201 / 40388815 = 0.4196 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 21:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.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 21:48:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:30: 1000000 INFO @ Sun, 21 Jun 2020 21:48:37: 2000000 INFO @ Sun, 21 Jun 2020 21:48:44: 3000000 INFO @ Sun, 21 Jun 2020 21:48:50: 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 @ Sun, 21 Jun 2020 21:48:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.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 21:48:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:58: 5000000 INFO @ Sun, 21 Jun 2020 21:49:01: 1000000 INFO @ Sun, 21 Jun 2020 21:49:05: 6000000 INFO @ Sun, 21 Jun 2020 21:49:08: 2000000 INFO @ Sun, 21 Jun 2020 21:49:12: 7000000 INFO @ Sun, 21 Jun 2020 21:49:15: 3000000 INFO @ Sun, 21 Jun 2020 21:49:20: 8000000 INFO @ Sun, 21 Jun 2020 21:49:22: 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 @ Sun, 21 Jun 2020 21:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.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 21:49:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:27: 9000000 INFO @ Sun, 21 Jun 2020 21:49:29: 5000000 INFO @ Sun, 21 Jun 2020 21:49:31: 1000000 INFO @ Sun, 21 Jun 2020 21:49:35: 10000000 INFO @ Sun, 21 Jun 2020 21:49:35: 6000000 INFO @ Sun, 21 Jun 2020 21:49:38: 2000000 INFO @ Sun, 21 Jun 2020 21:49:42: 7000000 INFO @ Sun, 21 Jun 2020 21:49:43: 11000000 INFO @ Sun, 21 Jun 2020 21:49:45: 3000000 INFO @ Sun, 21 Jun 2020 21:49:49: 8000000 INFO @ Sun, 21 Jun 2020 21:49:51: 12000000 INFO @ Sun, 21 Jun 2020 21:49:52: 4000000 INFO @ Sun, 21 Jun 2020 21:49:56: 9000000 INFO @ Sun, 21 Jun 2020 21:49:59: 13000000 INFO @ Sun, 21 Jun 2020 21:50:00: 5000000 INFO @ Sun, 21 Jun 2020 21:50:03: 10000000 INFO @ Sun, 21 Jun 2020 21:50:06: 14000000 INFO @ Sun, 21 Jun 2020 21:50:07: 6000000 INFO @ Sun, 21 Jun 2020 21:50:10: 11000000 INFO @ Sun, 21 Jun 2020 21:50:14: 15000000 INFO @ Sun, 21 Jun 2020 21:50:14: 7000000 INFO @ Sun, 21 Jun 2020 21:50:17: 12000000 INFO @ Sun, 21 Jun 2020 21:50:21: 8000000 INFO @ Sun, 21 Jun 2020 21:50:22: 16000000 INFO @ Sun, 21 Jun 2020 21:50:24: 13000000 INFO @ Sun, 21 Jun 2020 21:50:29: 9000000 INFO @ Sun, 21 Jun 2020 21:50:29: 17000000 INFO @ Sun, 21 Jun 2020 21:50:31: 14000000 INFO @ Sun, 21 Jun 2020 21:50:36: 10000000 INFO @ Sun, 21 Jun 2020 21:50:37: 18000000 INFO @ Sun, 21 Jun 2020 21:50:38: 15000000 INFO @ Sun, 21 Jun 2020 21:50:44: 11000000 INFO @ Sun, 21 Jun 2020 21:50:45: 16000000 INFO @ Sun, 21 Jun 2020 21:50:45: 19000000 INFO @ Sun, 21 Jun 2020 21:50:52: 12000000 INFO @ Sun, 21 Jun 2020 21:50:52: 17000000 INFO @ Sun, 21 Jun 2020 21:50:53: 20000000 INFO @ Sun, 21 Jun 2020 21:50:59: 18000000 INFO @ Sun, 21 Jun 2020 21:51:00: 13000000 INFO @ Sun, 21 Jun 2020 21:51:01: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:06: 19000000 INFO @ Sun, 21 Jun 2020 21:51:08: 14000000 INFO @ Sun, 21 Jun 2020 21:51:09: 22000000 INFO @ Sun, 21 Jun 2020 21:51:14: 20000000 INFO @ Sun, 21 Jun 2020 21:51:16: 15000000 INFO @ Sun, 21 Jun 2020 21:51:17: 23000000 INFO @ Sun, 21 Jun 2020 21:51:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:21: #1 total tags in treatment: 23442614 INFO @ Sun, 21 Jun 2020 21:51:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:21: #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 21:51:21: 21000000 INFO @ Sun, 21 Jun 2020 21:51:21: #1 tags after filtering in treatment: 23442553 INFO @ Sun, 21 Jun 2020 21:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:23: #2 number of paired peaks: 677 WARNING @ Sun, 21 Jun 2020 21:51:23: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:23: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:23: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:23: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:23: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:51:23: #2 alternative fragment length(s) may be 3,68 bps INFO @ Sun, 21 Jun 2020 21:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.05_model.r WARNING @ Sun, 21 Jun 2020 21:51:23: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:23: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Sun, 21 Jun 2020 21:51:23: #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 21:51:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:23: 16000000 INFO @ Sun, 21 Jun 2020 21:51:28: 22000000 INFO @ Sun, 21 Jun 2020 21:51:31: 17000000 INFO @ Sun, 21 Jun 2020 21:51:35: 23000000 INFO @ Sun, 21 Jun 2020 21:51:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:39: #1 total tags in treatment: 23442614 INFO @ Sun, 21 Jun 2020 21:51:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:39: #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 21:51:39: 18000000 INFO @ Sun, 21 Jun 2020 21:51:39: #1 tags after filtering in treatment: 23442553 INFO @ Sun, 21 Jun 2020 21:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:41: #2 number of paired peaks: 677 WARNING @ Sun, 21 Jun 2020 21:51:41: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:41: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:51:41: #2 alternative fragment length(s) may be 3,68 bps INFO @ Sun, 21 Jun 2020 21:51:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:41: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:41: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Sun, 21 Jun 2020 21:51:41: #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 21:51:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:47: 19000000 INFO @ Sun, 21 Jun 2020 21:51:54: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:01: 21000000 INFO @ Sun, 21 Jun 2020 21:52:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:09: 22000000 INFO @ Sun, 21 Jun 2020 21:52:16: 23000000 INFO @ Sun, 21 Jun 2020 21:52:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:52:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:52:20: #1 total tags in treatment: 23442614 INFO @ Sun, 21 Jun 2020 21:52:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:20: #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 21:52:20: #1 tags after filtering in treatment: 23442553 INFO @ Sun, 21 Jun 2020 21:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:22: #2 number of paired peaks: 677 WARNING @ Sun, 21 Jun 2020 21:52:22: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Sun, 21 Jun 2020 21:52:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:22: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:52:22: #2 alternative fragment length(s) may be 3,68 bps INFO @ Sun, 21 Jun 2020 21:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.20_model.r WARNING @ Sun, 21 Jun 2020 21:52:22: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:22: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Sun, 21 Jun 2020 21:52:22: #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 21:52:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.05_summits.bed INFO @ Sun, 21 Jun 2020 21:52:31: Done! pass1 - making usageList (757 chroms): 2 millis pass2 - checking and writing primary data (5204 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:49: Done! pass1 - making usageList (629 chroms): 2 millis pass2 - checking and writing primary data (3061 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:53:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011077/SRX5011077.20_summits.bed INFO @ Sun, 21 Jun 2020 21:53:32: Done! pass1 - making usageList (346 chroms): 1 millis pass2 - checking and writing primary data (1120 records, 4 fields): 23 millis CompletedMACS2peakCalling