Job ID = 6527614 SRX = SRX1433395 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:39:11 prefetch.2.10.7: 1) Downloading 'SRR2919811'... 2020-06-29T12:39:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:42:29 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:42:29 prefetch.2.10.7: 1) 'SRR2919811' was downloaded successfully Read 41218324 spots for SRR2919811/SRR2919811.sra Written 41218324 spots for SRR2919811/SRR2919811.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: 00:11:14 41218324 reads; of these: 41218324 (100.00%) were unpaired; of these: 1264894 (3.07%) aligned 0 times 29381687 (71.28%) aligned exactly 1 time 10571743 (25.65%) aligned >1 times 96.93% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 9011266 / 39953430 = 0.2255 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 @ Mon, 29 Jun 2020 22:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.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 @ Mon, 29 Jun 2020 22:08:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:08:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:08:20: 1000000 INFO @ Mon, 29 Jun 2020 22:08:24: 2000000 INFO @ Mon, 29 Jun 2020 22:08:28: 3000000 INFO @ Mon, 29 Jun 2020 22:08:33: 4000000 INFO @ Mon, 29 Jun 2020 22:08:37: 5000000 INFO @ Mon, 29 Jun 2020 22:08:42: 6000000 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 @ Mon, 29 Jun 2020 22:08:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.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 @ Mon, 29 Jun 2020 22:08:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:08:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:08:46: 7000000 INFO @ Mon, 29 Jun 2020 22:08:50: 1000000 INFO @ Mon, 29 Jun 2020 22:08:50: 8000000 INFO @ Mon, 29 Jun 2020 22:08:55: 2000000 INFO @ Mon, 29 Jun 2020 22:08:55: 9000000 INFO @ Mon, 29 Jun 2020 22:08:59: 3000000 INFO @ Mon, 29 Jun 2020 22:08:59: 10000000 INFO @ Mon, 29 Jun 2020 22:09:04: 4000000 INFO @ Mon, 29 Jun 2020 22:09:04: 11000000 INFO @ Mon, 29 Jun 2020 22:09:08: 12000000 INFO @ Mon, 29 Jun 2020 22:09:08: 5000000 INFO @ Mon, 29 Jun 2020 22:09:13: 13000000 INFO @ Mon, 29 Jun 2020 22:09:13: 6000000 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 @ Mon, 29 Jun 2020 22:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.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 @ Mon, 29 Jun 2020 22:09:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:09:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:09:17: 14000000 INFO @ Mon, 29 Jun 2020 22:09:17: 7000000 INFO @ Mon, 29 Jun 2020 22:09:20: 1000000 INFO @ Mon, 29 Jun 2020 22:09:22: 15000000 INFO @ Mon, 29 Jun 2020 22:09:22: 8000000 INFO @ Mon, 29 Jun 2020 22:09:25: 2000000 INFO @ Mon, 29 Jun 2020 22:09:26: 16000000 INFO @ Mon, 29 Jun 2020 22:09:27: 9000000 INFO @ Mon, 29 Jun 2020 22:09:29: 3000000 INFO @ Mon, 29 Jun 2020 22:09:31: 17000000 INFO @ Mon, 29 Jun 2020 22:09:31: 10000000 INFO @ Mon, 29 Jun 2020 22:09:34: 4000000 INFO @ Mon, 29 Jun 2020 22:09:35: 18000000 INFO @ Mon, 29 Jun 2020 22:09:36: 11000000 INFO @ Mon, 29 Jun 2020 22:09:38: 5000000 INFO @ Mon, 29 Jun 2020 22:09:40: 19000000 INFO @ Mon, 29 Jun 2020 22:09:40: 12000000 INFO @ Mon, 29 Jun 2020 22:09:43: 6000000 INFO @ Mon, 29 Jun 2020 22:09:44: 20000000 INFO @ Mon, 29 Jun 2020 22:09:45: 13000000 INFO @ Mon, 29 Jun 2020 22:09:47: 7000000 INFO @ Mon, 29 Jun 2020 22:09:49: 21000000 INFO @ Mon, 29 Jun 2020 22:09:49: 14000000 INFO @ Mon, 29 Jun 2020 22:09:52: 8000000 INFO @ Mon, 29 Jun 2020 22:09:53: 22000000 INFO @ Mon, 29 Jun 2020 22:09:54: 15000000 INFO @ Mon, 29 Jun 2020 22:09:57: 9000000 INFO @ Mon, 29 Jun 2020 22:09:58: 23000000 INFO @ Mon, 29 Jun 2020 22:09:58: 16000000 INFO @ Mon, 29 Jun 2020 22:10:01: 10000000 INFO @ Mon, 29 Jun 2020 22:10:02: 24000000 INFO @ Mon, 29 Jun 2020 22:10:03: 17000000 INFO @ Mon, 29 Jun 2020 22:10:06: 11000000 INFO @ Mon, 29 Jun 2020 22:10:07: 25000000 INFO @ Mon, 29 Jun 2020 22:10:07: 18000000 INFO @ Mon, 29 Jun 2020 22:10:10: 12000000 INFO @ Mon, 29 Jun 2020 22:10:11: 26000000 INFO @ Mon, 29 Jun 2020 22:10:12: 19000000 INFO @ Mon, 29 Jun 2020 22:10:15: 13000000 INFO @ Mon, 29 Jun 2020 22:10:16: 27000000 INFO @ Mon, 29 Jun 2020 22:10:16: 20000000 INFO @ Mon, 29 Jun 2020 22:10:19: 14000000 INFO @ Mon, 29 Jun 2020 22:10:20: 28000000 INFO @ Mon, 29 Jun 2020 22:10:21: 21000000 INFO @ Mon, 29 Jun 2020 22:10:24: 15000000 INFO @ Mon, 29 Jun 2020 22:10:25: 29000000 INFO @ Mon, 29 Jun 2020 22:10:26: 22000000 INFO @ Mon, 29 Jun 2020 22:10:28: 16000000 INFO @ Mon, 29 Jun 2020 22:10:29: 30000000 INFO @ Mon, 29 Jun 2020 22:10:30: 23000000 INFO @ Mon, 29 Jun 2020 22:10:33: 17000000 INFO @ Mon, 29 Jun 2020 22:10:34: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 22:10:34: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 22:10:34: #1 total tags in treatment: 30942164 INFO @ Mon, 29 Jun 2020 22:10:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:10:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:10:34: #1 tags after filtering in treatment: 30942164 INFO @ Mon, 29 Jun 2020 22:10:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:10:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:10:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:10:35: 24000000 INFO @ Mon, 29 Jun 2020 22:10:36: #2 number of paired peaks: 144 WARNING @ Mon, 29 Jun 2020 22:10:36: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 29 Jun 2020 22:10:36: start model_add_line... INFO @ Mon, 29 Jun 2020 22:10:36: start X-correlation... INFO @ Mon, 29 Jun 2020 22:10:36: end of X-cor INFO @ Mon, 29 Jun 2020 22:10:36: #2 finished! INFO @ Mon, 29 Jun 2020 22:10:36: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 22:10:36: #2 alternative fragment length(s) may be 2,41,567,571,574,586 bps INFO @ Mon, 29 Jun 2020 22:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.05_model.r WARNING @ Mon, 29 Jun 2020 22:10:36: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:10:36: #2 You may need to consider one of the other alternative d(s): 2,41,567,571,574,586 WARNING @ Mon, 29 Jun 2020 22:10:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:10:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:10:37: 18000000 INFO @ Mon, 29 Jun 2020 22:10:39: 25000000 INFO @ Mon, 29 Jun 2020 22:10:42: 19000000 INFO @ Mon, 29 Jun 2020 22:10:44: 26000000 INFO @ Mon, 29 Jun 2020 22:10:46: 20000000 INFO @ Mon, 29 Jun 2020 22:10:48: 27000000 INFO @ Mon, 29 Jun 2020 22:10:51: 21000000 INFO @ Mon, 29 Jun 2020 22:10:53: 28000000 INFO @ Mon, 29 Jun 2020 22:10:55: 22000000 INFO @ Mon, 29 Jun 2020 22:10:57: 29000000 INFO @ Mon, 29 Jun 2020 22:11:00: 23000000 INFO @ Mon, 29 Jun 2020 22:11:02: 30000000 INFO @ Mon, 29 Jun 2020 22:11:04: 24000000 INFO @ Mon, 29 Jun 2020 22:11:06: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 22:11:06: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 22:11:06: #1 total tags in treatment: 30942164 INFO @ Mon, 29 Jun 2020 22:11:06: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:11:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:11:07: #1 tags after filtering in treatment: 30942164 INFO @ Mon, 29 Jun 2020 22:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:11:07: #1 finished! INFO @ Mon, 29 Jun 2020 22:11:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:11:09: #2 number of paired peaks: 144 WARNING @ Mon, 29 Jun 2020 22:11:09: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 29 Jun 2020 22:11:09: start model_add_line... INFO @ Mon, 29 Jun 2020 22:11:09: start X-correlation... INFO @ Mon, 29 Jun 2020 22:11:09: end of X-cor INFO @ Mon, 29 Jun 2020 22:11:09: #2 finished! INFO @ Mon, 29 Jun 2020 22:11:09: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 22:11:09: #2 alternative fragment length(s) may be 2,41,567,571,574,586 bps INFO @ Mon, 29 Jun 2020 22:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.10_model.r WARNING @ Mon, 29 Jun 2020 22:11:09: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:11:09: #2 You may need to consider one of the other alternative d(s): 2,41,567,571,574,586 WARNING @ Mon, 29 Jun 2020 22:11:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:11:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:11:09: 25000000 INFO @ Mon, 29 Jun 2020 22:11:13: 26000000 INFO @ Mon, 29 Jun 2020 22:11:18: 27000000 INFO @ Mon, 29 Jun 2020 22:11:22: 28000000 INFO @ Mon, 29 Jun 2020 22:11:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:11:27: 29000000 INFO @ Mon, 29 Jun 2020 22:11:31: 30000000 INFO @ Mon, 29 Jun 2020 22:11:35: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 22:11:35: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 22:11:35: #1 total tags in treatment: 30942164 INFO @ Mon, 29 Jun 2020 22:11:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:11:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:11:36: #1 tags after filtering in treatment: 30942164 INFO @ Mon, 29 Jun 2020 22:11:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:11:36: #1 finished! INFO @ Mon, 29 Jun 2020 22:11:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:11:38: #2 number of paired peaks: 144 WARNING @ Mon, 29 Jun 2020 22:11:38: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Mon, 29 Jun 2020 22:11:38: start model_add_line... INFO @ Mon, 29 Jun 2020 22:11:38: start X-correlation... INFO @ Mon, 29 Jun 2020 22:11:38: end of X-cor INFO @ Mon, 29 Jun 2020 22:11:38: #2 finished! INFO @ Mon, 29 Jun 2020 22:11:38: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 22:11:38: #2 alternative fragment length(s) may be 2,41,567,571,574,586 bps INFO @ Mon, 29 Jun 2020 22:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.20_model.r WARNING @ Mon, 29 Jun 2020 22:11:38: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:11:38: #2 You may need to consider one of the other alternative d(s): 2,41,567,571,574,586 WARNING @ Mon, 29 Jun 2020 22:11:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:11:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.05_summits.bed INFO @ Mon, 29 Jun 2020 22:11:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3767 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:12:00: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.10_summits.bed INFO @ Mon, 29 Jun 2020 22:12:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2498 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:12:28: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1433395/SRX1433395.20_summits.bed INFO @ Mon, 29 Jun 2020 22:12:52: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1280 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。