Job ID = 6527723 SRX = SRX2520651 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:18:24 prefetch.2.10.7: 1) Downloading 'SRR5206770'... 2020-06-29T13:18:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:34:19 prefetch.2.10.7: HTTPS download failed 2020-06-29T13:34:19 prefetch.2.10.7: 1) failed to download SRR5206770 2020-06-29T13:34:29 prefetch.2.10.7: 1) Downloading 'SRR5206770'... 2020-06-29T13:34:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:34:29 prefetch.2.10.7: Continue download of 'SRR5206770' from 1624809689 2020-06-29T13:34:34 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:34:34 prefetch.2.10.7: 1) 'SRR5206770' was downloaded successfully Read 33813091 spots for SRR5206770/SRR5206770.sra Written 33813091 spots for SRR5206770/SRR5206770.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: 00:08:11 33813091 reads; of these: 33813091 (100.00%) were unpaired; of these: 499485 (1.48%) aligned 0 times 27929337 (82.60%) aligned exactly 1 time 5384269 (15.92%) aligned >1 times 98.52% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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 16 files... [bam_rmdupse_core] 17584317 / 33313606 = 0.5278 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 23:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.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 23:00:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:00:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:00:57: 1000000 INFO @ Mon, 29 Jun 2020 23:01:03: 2000000 INFO @ Mon, 29 Jun 2020 23:01:08: 3000000 INFO @ Mon, 29 Jun 2020 23:01:13: 4000000 INFO @ Mon, 29 Jun 2020 23:01:19: 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 @ Mon, 29 Jun 2020 23:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.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 23:01:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:01:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:01:24: 6000000 INFO @ Mon, 29 Jun 2020 23:01:28: 1000000 INFO @ Mon, 29 Jun 2020 23:01:30: 7000000 INFO @ Mon, 29 Jun 2020 23:01:34: 2000000 INFO @ Mon, 29 Jun 2020 23:01:36: 8000000 INFO @ Mon, 29 Jun 2020 23:01:40: 3000000 INFO @ Mon, 29 Jun 2020 23:01:42: 9000000 INFO @ Mon, 29 Jun 2020 23:01:46: 4000000 INFO @ Mon, 29 Jun 2020 23:01:48: 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 @ Mon, 29 Jun 2020 23:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.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 23:01:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:01:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:01:52: 5000000 INFO @ Mon, 29 Jun 2020 23:01:54: 11000000 INFO @ Mon, 29 Jun 2020 23:01:58: 1000000 INFO @ Mon, 29 Jun 2020 23:01:59: 6000000 INFO @ Mon, 29 Jun 2020 23:02:01: 12000000 INFO @ Mon, 29 Jun 2020 23:02:04: 2000000 INFO @ Mon, 29 Jun 2020 23:02:06: 7000000 INFO @ Mon, 29 Jun 2020 23:02:07: 13000000 INFO @ Mon, 29 Jun 2020 23:02:11: 3000000 INFO @ Mon, 29 Jun 2020 23:02:13: 8000000 INFO @ Mon, 29 Jun 2020 23:02:13: 14000000 INFO @ Mon, 29 Jun 2020 23:02:17: 4000000 INFO @ Mon, 29 Jun 2020 23:02:19: 9000000 INFO @ Mon, 29 Jun 2020 23:02:20: 15000000 INFO @ Mon, 29 Jun 2020 23:02:23: 5000000 INFO @ Mon, 29 Jun 2020 23:02:24: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:02:24: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:02:24: #1 total tags in treatment: 15729289 INFO @ Mon, 29 Jun 2020 23:02:24: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:02:24: #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 23:02:25: #1 tags after filtering in treatment: 15729289 INFO @ Mon, 29 Jun 2020 23:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:02:25: #1 finished! INFO @ Mon, 29 Jun 2020 23:02:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:02:26: 10000000 INFO @ Mon, 29 Jun 2020 23:02:26: #2 number of paired peaks: 968 WARNING @ Mon, 29 Jun 2020 23:02:26: Fewer paired peaks (968) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 968 pairs to build model! INFO @ Mon, 29 Jun 2020 23:02:26: start model_add_line... INFO @ Mon, 29 Jun 2020 23:02:26: start X-correlation... INFO @ Mon, 29 Jun 2020 23:02:26: end of X-cor INFO @ Mon, 29 Jun 2020 23:02:26: #2 finished! INFO @ Mon, 29 Jun 2020 23:02:26: #2 predicted fragment length is 121 bps INFO @ Mon, 29 Jun 2020 23:02:26: #2 alternative fragment length(s) may be 0,11,14,24,105,121 bps INFO @ Mon, 29 Jun 2020 23:02:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.05_model.r INFO @ Mon, 29 Jun 2020 23:02:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:02:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:02:29: 6000000 INFO @ Mon, 29 Jun 2020 23:02:33: 11000000 INFO @ Mon, 29 Jun 2020 23:02:35: 7000000 INFO @ Mon, 29 Jun 2020 23:02:40: 12000000 INFO @ Mon, 29 Jun 2020 23:02:41: 8000000 INFO @ Mon, 29 Jun 2020 23:02:47: 13000000 INFO @ Mon, 29 Jun 2020 23:02:47: 9000000 INFO @ Mon, 29 Jun 2020 23:02:54: 14000000 INFO @ Mon, 29 Jun 2020 23:02:54: 10000000 INFO @ Mon, 29 Jun 2020 23:02:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:03:00: 11000000 INFO @ Mon, 29 Jun 2020 23:03:00: 15000000 INFO @ Mon, 29 Jun 2020 23:03:05: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:03:05: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:03:05: #1 total tags in treatment: 15729289 INFO @ Mon, 29 Jun 2020 23:03:05: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:05: #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 23:03:06: #1 tags after filtering in treatment: 15729289 INFO @ Mon, 29 Jun 2020 23:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:03:06: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:06: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:07: 12000000 INFO @ Mon, 29 Jun 2020 23:03:07: #2 number of paired peaks: 968 WARNING @ Mon, 29 Jun 2020 23:03:07: Fewer paired peaks (968) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 968 pairs to build model! INFO @ Mon, 29 Jun 2020 23:03:07: start model_add_line... INFO @ Mon, 29 Jun 2020 23:03:07: start X-correlation... INFO @ Mon, 29 Jun 2020 23:03:07: end of X-cor INFO @ Mon, 29 Jun 2020 23:03:07: #2 finished! INFO @ Mon, 29 Jun 2020 23:03:07: #2 predicted fragment length is 121 bps INFO @ Mon, 29 Jun 2020 23:03:07: #2 alternative fragment length(s) may be 0,11,14,24,105,121 bps INFO @ Mon, 29 Jun 2020 23:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.10_model.r INFO @ Mon, 29 Jun 2020 23:03:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:03:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:03:13: 13000000 INFO @ Mon, 29 Jun 2020 23:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.05_summits.bed INFO @ Mon, 29 Jun 2020 23:03:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7221 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:03:20: 14000000 INFO @ Mon, 29 Jun 2020 23:03:26: 15000000 INFO @ Mon, 29 Jun 2020 23:03:31: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:03:31: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:03:31: #1 total tags in treatment: 15729289 INFO @ Mon, 29 Jun 2020 23:03:31: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:31: #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 23:03:31: #1 tags after filtering in treatment: 15729289 INFO @ Mon, 29 Jun 2020 23:03:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:03:31: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:32: #2 number of paired peaks: 968 WARNING @ Mon, 29 Jun 2020 23:03:32: Fewer paired peaks (968) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 968 pairs to build model! INFO @ Mon, 29 Jun 2020 23:03:32: start model_add_line... INFO @ Mon, 29 Jun 2020 23:03:32: start X-correlation... INFO @ Mon, 29 Jun 2020 23:03:32: end of X-cor INFO @ Mon, 29 Jun 2020 23:03:32: #2 finished! INFO @ Mon, 29 Jun 2020 23:03:32: #2 predicted fragment length is 121 bps INFO @ Mon, 29 Jun 2020 23:03:32: #2 alternative fragment length(s) may be 0,11,14,24,105,121 bps INFO @ Mon, 29 Jun 2020 23:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.20_model.r INFO @ Mon, 29 Jun 2020 23:03:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:03:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.10_summits.bed INFO @ Mon, 29 Jun 2020 23:03:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2385 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:04:04: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:04:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:04:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:04:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2520651/SRX2520651.20_summits.bed INFO @ Mon, 29 Jun 2020 23:04:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling