Job ID = 6527857 SRX = SRX287886 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:55:19 prefetch.2.10.7: 1) Downloading 'SRR870075'... 2020-06-29T13:55:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:58:08 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:58:08 prefetch.2.10.7: 1) 'SRR870075' was downloaded successfully Read 21494133 spots for SRR870075/SRR870075.sra Written 21494133 spots for SRR870075/SRR870075.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: 00:09:23 21494133 reads; of these: 21494133 (100.00%) were unpaired; of these: 1285007 (5.98%) aligned 0 times 13473096 (62.68%) aligned exactly 1 time 6736030 (31.34%) aligned >1 times 94.02% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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 12 files... [bam_rmdupse_core] 3043355 / 20209126 = 0.1506 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 23:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.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 23:21:35: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:21:35: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:21:44: 1000000 INFO @ Mon, 29 Jun 2020 23:21:54: 2000000 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 23:22:03: 3000000 INFO @ Mon, 29 Jun 2020 23:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.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 23:22:05: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:22:05: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:22:12: 4000000 INFO @ Mon, 29 Jun 2020 23:22:14: 1000000 INFO @ Mon, 29 Jun 2020 23:22:21: 5000000 INFO @ Mon, 29 Jun 2020 23:22:23: 2000000 INFO @ Mon, 29 Jun 2020 23:22:30: 6000000 INFO @ Mon, 29 Jun 2020 23:22:32: 3000000 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 23:22:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.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 23:22:35: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:22:35: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:22:39: 7000000 INFO @ Mon, 29 Jun 2020 23:22:40: 4000000 INFO @ Mon, 29 Jun 2020 23:22:44: 1000000 INFO @ Mon, 29 Jun 2020 23:22:48: 8000000 INFO @ Mon, 29 Jun 2020 23:22:49: 5000000 INFO @ Mon, 29 Jun 2020 23:22:53: 2000000 INFO @ Mon, 29 Jun 2020 23:22:56: 9000000 INFO @ Mon, 29 Jun 2020 23:22:58: 6000000 INFO @ Mon, 29 Jun 2020 23:23:02: 3000000 INFO @ Mon, 29 Jun 2020 23:23:05: 10000000 INFO @ Mon, 29 Jun 2020 23:23:07: 7000000 INFO @ Mon, 29 Jun 2020 23:23:11: 4000000 INFO @ Mon, 29 Jun 2020 23:23:14: 11000000 INFO @ Mon, 29 Jun 2020 23:23:16: 8000000 INFO @ Mon, 29 Jun 2020 23:23:20: 5000000 INFO @ Mon, 29 Jun 2020 23:23:23: 12000000 INFO @ Mon, 29 Jun 2020 23:23:25: 9000000 INFO @ Mon, 29 Jun 2020 23:23:29: 6000000 INFO @ Mon, 29 Jun 2020 23:23:33: 13000000 INFO @ Mon, 29 Jun 2020 23:23:34: 10000000 INFO @ Mon, 29 Jun 2020 23:23:38: 7000000 INFO @ Mon, 29 Jun 2020 23:23:41: 14000000 INFO @ Mon, 29 Jun 2020 23:23:43: 11000000 INFO @ Mon, 29 Jun 2020 23:23:47: 8000000 INFO @ Mon, 29 Jun 2020 23:23:51: 15000000 INFO @ Mon, 29 Jun 2020 23:23:52: 12000000 INFO @ Mon, 29 Jun 2020 23:23:55: 9000000 INFO @ Mon, 29 Jun 2020 23:24:00: 16000000 INFO @ Mon, 29 Jun 2020 23:24:01: 13000000 INFO @ Mon, 29 Jun 2020 23:24:04: 10000000 INFO @ Mon, 29 Jun 2020 23:24:09: 17000000 INFO @ Mon, 29 Jun 2020 23:24:10: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:24:10: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:24:10: #1 total tags in treatment: 17165771 INFO @ Mon, 29 Jun 2020 23:24:10: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:24:10: #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 23:24:10: 14000000 INFO @ Mon, 29 Jun 2020 23:24:11: #1 tags after filtering in treatment: 17165771 INFO @ Mon, 29 Jun 2020 23:24:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:24:11: #1 finished! INFO @ Mon, 29 Jun 2020 23:24:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:24:12: #2 number of paired peaks: 198 WARNING @ Mon, 29 Jun 2020 23:24:12: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 29 Jun 2020 23:24:12: start model_add_line... INFO @ Mon, 29 Jun 2020 23:24:12: start X-correlation... INFO @ Mon, 29 Jun 2020 23:24:12: end of X-cor INFO @ Mon, 29 Jun 2020 23:24:12: #2 finished! INFO @ Mon, 29 Jun 2020 23:24:12: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:24:12: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:24:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.05_model.r WARNING @ Mon, 29 Jun 2020 23:24:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:24:12: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:24:12: #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 23:24:12: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:24:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:24:13: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:24:19: 15000000 INFO @ Mon, 29 Jun 2020 23:24:22: 12000000 INFO @ Mon, 29 Jun 2020 23:24:27: 16000000 INFO @ Mon, 29 Jun 2020 23:24:31: 13000000 INFO @ Mon, 29 Jun 2020 23:24:36: 17000000 INFO @ Mon, 29 Jun 2020 23:24:38: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:24:38: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:24:38: #1 total tags in treatment: 17165771 INFO @ Mon, 29 Jun 2020 23:24:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:24:38: #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 23:24:38: #1 tags after filtering in treatment: 17165771 INFO @ Mon, 29 Jun 2020 23:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:24:38: #1 finished! INFO @ Mon, 29 Jun 2020 23:24:38: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:24:39: #2 number of paired peaks: 198 WARNING @ Mon, 29 Jun 2020 23:24:39: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 29 Jun 2020 23:24:39: start model_add_line... INFO @ Mon, 29 Jun 2020 23:24:39: start X-correlation... INFO @ Mon, 29 Jun 2020 23:24:39: end of X-cor INFO @ Mon, 29 Jun 2020 23:24:39: #2 finished! INFO @ Mon, 29 Jun 2020 23:24:39: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:24:39: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.10_model.r WARNING @ Mon, 29 Jun 2020 23:24:39: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:24:39: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:24:39: #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 23:24:39: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:24:40: 14000000 INFO @ Mon, 29 Jun 2020 23:24:41: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:24:49: 15000000 INFO @ Mon, 29 Jun 2020 23:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:24:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:24:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.05_summits.bed INFO @ Mon, 29 Jun 2020 23:24:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2203 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:24:57: 16000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:25:06: 17000000 INFO @ Mon, 29 Jun 2020 23:25:07: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:25:07: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:25:07: #1 total tags in treatment: 17165771 INFO @ Mon, 29 Jun 2020 23:25:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:25:07: #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 23:25:08: #1 tags after filtering in treatment: 17165771 INFO @ Mon, 29 Jun 2020 23:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:25:08: #1 finished! INFO @ Mon, 29 Jun 2020 23:25:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:25:09: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:25:09: #2 number of paired peaks: 198 WARNING @ Mon, 29 Jun 2020 23:25:09: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Mon, 29 Jun 2020 23:25:09: start model_add_line... INFO @ Mon, 29 Jun 2020 23:25:09: start X-correlation... INFO @ Mon, 29 Jun 2020 23:25:09: end of X-cor INFO @ Mon, 29 Jun 2020 23:25:09: #2 finished! INFO @ Mon, 29 Jun 2020 23:25:09: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 23:25:09: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 23:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.20_model.r WARNING @ Mon, 29 Jun 2020 23:25:09: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:25:09: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 23:25:09: #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 23:25:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:25:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:25:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:25:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.10_summits.bed INFO @ Mon, 29 Jun 2020 23:25:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:25:38: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:25:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:25:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:25:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287886/SRX287886.20_summits.bed INFO @ Mon, 29 Jun 2020 23:25:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1311 records, 4 fields): 133 millis CompletedMACS2peakCalling