Job ID = 6529682 SRX = SRX3981659 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:10:53 39319285 reads; of these: 39319285 (100.00%) were unpaired; of these: 1362621 (3.47%) aligned 0 times 27919575 (71.01%) aligned exactly 1 time 10037089 (25.53%) aligned >1 times 96.53% overall alignment rate Time searching: 00:10:53 Overall time: 00:10:53 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 16 files... [bam_rmdupse_core] 5263921 / 37956664 = 0.1387 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, 30 Jun 2020 02:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.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 @ Tue, 30 Jun 2020 02:45:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:56: 1000000 INFO @ Tue, 30 Jun 2020 02:46:03: 2000000 INFO @ Tue, 30 Jun 2020 02:46:10: 3000000 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, 30 Jun 2020 02:46:17: 4000000 INFO @ Tue, 30 Jun 2020 02:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.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 @ Tue, 30 Jun 2020 02:46:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:24: 5000000 INFO @ Tue, 30 Jun 2020 02:46:24: 1000000 INFO @ Tue, 30 Jun 2020 02:46:29: 2000000 INFO @ Tue, 30 Jun 2020 02:46:31: 6000000 INFO @ Tue, 30 Jun 2020 02:46:35: 3000000 INFO @ Tue, 30 Jun 2020 02:46:37: 7000000 INFO @ Tue, 30 Jun 2020 02:46:40: 4000000 INFO @ Tue, 30 Jun 2020 02:46:44: 8000000 INFO @ Tue, 30 Jun 2020 02:46:46: 5000000 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, 30 Jun 2020 02:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.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 @ Tue, 30 Jun 2020 02:46:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:51: 6000000 INFO @ Tue, 30 Jun 2020 02:46:51: 9000000 INFO @ Tue, 30 Jun 2020 02:46:56: 1000000 INFO @ Tue, 30 Jun 2020 02:46:56: 7000000 INFO @ Tue, 30 Jun 2020 02:46:58: 10000000 INFO @ Tue, 30 Jun 2020 02:47:02: 8000000 INFO @ Tue, 30 Jun 2020 02:47:03: 2000000 INFO @ Tue, 30 Jun 2020 02:47:05: 11000000 INFO @ Tue, 30 Jun 2020 02:47:07: 9000000 INFO @ Tue, 30 Jun 2020 02:47:10: 3000000 INFO @ Tue, 30 Jun 2020 02:47:12: 12000000 INFO @ Tue, 30 Jun 2020 02:47:13: 10000000 INFO @ Tue, 30 Jun 2020 02:47:17: 4000000 INFO @ Tue, 30 Jun 2020 02:47:18: 11000000 INFO @ Tue, 30 Jun 2020 02:47:19: 13000000 INFO @ Tue, 30 Jun 2020 02:47:23: 5000000 INFO @ Tue, 30 Jun 2020 02:47:24: 12000000 INFO @ Tue, 30 Jun 2020 02:47:26: 14000000 INFO @ Tue, 30 Jun 2020 02:47:29: 13000000 INFO @ Tue, 30 Jun 2020 02:47:30: 6000000 INFO @ Tue, 30 Jun 2020 02:47:33: 15000000 INFO @ Tue, 30 Jun 2020 02:47:34: 14000000 INFO @ Tue, 30 Jun 2020 02:47:37: 7000000 INFO @ Tue, 30 Jun 2020 02:47:40: 15000000 INFO @ Tue, 30 Jun 2020 02:47:40: 16000000 INFO @ Tue, 30 Jun 2020 02:47:44: 8000000 INFO @ Tue, 30 Jun 2020 02:47:45: 16000000 INFO @ Tue, 30 Jun 2020 02:47:47: 17000000 INFO @ Tue, 30 Jun 2020 02:47:50: 17000000 INFO @ Tue, 30 Jun 2020 02:47:51: 9000000 INFO @ Tue, 30 Jun 2020 02:47:54: 18000000 INFO @ Tue, 30 Jun 2020 02:47:56: 18000000 INFO @ Tue, 30 Jun 2020 02:47:58: 10000000 INFO @ Tue, 30 Jun 2020 02:48:01: 19000000 INFO @ Tue, 30 Jun 2020 02:48:01: 19000000 INFO @ Tue, 30 Jun 2020 02:48:05: 11000000 INFO @ Tue, 30 Jun 2020 02:48:07: 20000000 INFO @ Tue, 30 Jun 2020 02:48:08: 20000000 INFO @ Tue, 30 Jun 2020 02:48:11: 12000000 INFO @ Tue, 30 Jun 2020 02:48:12: 21000000 INFO @ Tue, 30 Jun 2020 02:48:14: 21000000 INFO @ Tue, 30 Jun 2020 02:48:17: 22000000 INFO @ Tue, 30 Jun 2020 02:48:18: 13000000 INFO @ Tue, 30 Jun 2020 02:48:21: 22000000 INFO @ Tue, 30 Jun 2020 02:48:23: 23000000 INFO @ Tue, 30 Jun 2020 02:48:25: 14000000 INFO @ Tue, 30 Jun 2020 02:48:28: 23000000 INFO @ Tue, 30 Jun 2020 02:48:28: 24000000 INFO @ Tue, 30 Jun 2020 02:48:32: 15000000 INFO @ Tue, 30 Jun 2020 02:48:33: 25000000 INFO @ Tue, 30 Jun 2020 02:48:35: 24000000 INFO @ Tue, 30 Jun 2020 02:48:39: 16000000 INFO @ Tue, 30 Jun 2020 02:48:39: 26000000 INFO @ Tue, 30 Jun 2020 02:48:42: 25000000 INFO @ Tue, 30 Jun 2020 02:48:44: 27000000 INFO @ Tue, 30 Jun 2020 02:48:46: 17000000 INFO @ Tue, 30 Jun 2020 02:48:49: 26000000 INFO @ Tue, 30 Jun 2020 02:48:51: 28000000 INFO @ Tue, 30 Jun 2020 02:48:53: 18000000 INFO @ Tue, 30 Jun 2020 02:48:56: 27000000 INFO @ Tue, 30 Jun 2020 02:48:56: 29000000 INFO @ Tue, 30 Jun 2020 02:48:59: 19000000 INFO @ Tue, 30 Jun 2020 02:49:01: 30000000 INFO @ Tue, 30 Jun 2020 02:49:03: 28000000 INFO @ Tue, 30 Jun 2020 02:49:06: 20000000 INFO @ Tue, 30 Jun 2020 02:49:07: 31000000 INFO @ Tue, 30 Jun 2020 02:49:10: 29000000 INFO @ Tue, 30 Jun 2020 02:49:12: 32000000 INFO @ Tue, 30 Jun 2020 02:49:13: 21000000 INFO @ Tue, 30 Jun 2020 02:49:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:49:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:49:17: #1 total tags in treatment: 32692743 INFO @ Tue, 30 Jun 2020 02:49:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:49:17: 30000000 INFO @ Tue, 30 Jun 2020 02:49:18: #1 tags after filtering in treatment: 32692704 INFO @ Tue, 30 Jun 2020 02:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:20: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 02:49:20: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:20: 22000000 INFO @ Tue, 30 Jun 2020 02:49:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:20: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:49:20: #2 alternative fragment length(s) may be 1,51,594,597 bps INFO @ Tue, 30 Jun 2020 02:49:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.10_model.r WARNING @ Tue, 30 Jun 2020 02:49:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:20: #2 You may need to consider one of the other alternative d(s): 1,51,594,597 WARNING @ Tue, 30 Jun 2020 02:49:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:49:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:24: 31000000 INFO @ Tue, 30 Jun 2020 02:49:27: 23000000 INFO @ Tue, 30 Jun 2020 02:49:31: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:49:33: 24000000 INFO @ Tue, 30 Jun 2020 02:49:36: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:49:36: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:49:36: #1 total tags in treatment: 32692743 INFO @ Tue, 30 Jun 2020 02:49:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:49:37: #1 tags after filtering in treatment: 32692704 INFO @ Tue, 30 Jun 2020 02:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:39: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 02:49:39: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:40: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:49:40: #2 alternative fragment length(s) may be 1,51,594,597 bps INFO @ Tue, 30 Jun 2020 02:49:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:40: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:40: #2 You may need to consider one of the other alternative d(s): 1,51,594,597 WARNING @ Tue, 30 Jun 2020 02:49:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:49:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:40: 25000000 INFO @ Tue, 30 Jun 2020 02:49:46: 26000000 INFO @ Tue, 30 Jun 2020 02:49:53: 27000000 INFO @ Tue, 30 Jun 2020 02:50:00: 28000000 INFO @ Tue, 30 Jun 2020 02:50:06: 29000000 INFO @ Tue, 30 Jun 2020 02:50:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:12: 30000000 INFO @ Tue, 30 Jun 2020 02:50:18: 31000000 INFO @ Tue, 30 Jun 2020 02:50:25: 32000000 INFO @ Tue, 30 Jun 2020 02:50:30: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:50:30: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:50:30: #1 total tags in treatment: 32692743 INFO @ Tue, 30 Jun 2020 02:50:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:50:31: #1 tags after filtering in treatment: 32692704 INFO @ Tue, 30 Jun 2020 02:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:31: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:33: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 02:50:33: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:33: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:50:33: #2 alternative fragment length(s) may be 1,51,594,597 bps INFO @ Tue, 30 Jun 2020 02:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:33: #2 You may need to consider one of the other alternative d(s): 1,51,594,597 WARNING @ Tue, 30 Jun 2020 02:50:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:50:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.10_summits.bed INFO @ Tue, 30 Jun 2020 02:50:38: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (2017 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:59: Done! pass1 - making usageList (661 chroms): 1 millis pass2 - checking and writing primary data (3281 records, 4 fields): 39 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981659/SRX3981659.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:53: Done! pass1 - making usageList (277 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 17 millis CompletedMACS2peakCalling