Job ID = 6455557 SRX = SRX287883 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:40 prefetch.2.10.7: 1) Downloading 'SRR870072'... 2020-06-21T10:05:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:07:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:07:04 prefetch.2.10.7: 'SRR870072' is valid 2020-06-21T10:07:04 prefetch.2.10.7: 1) 'SRR870072' was downloaded successfully Read 11134459 spots for SRR870072/SRR870072.sra Written 11134459 spots for SRR870072/SRR870072.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: 00:03:00 11134459 reads; of these: 11134459 (100.00%) were unpaired; of these: 758955 (6.82%) aligned 0 times 7777104 (69.85%) aligned exactly 1 time 2598400 (23.34%) aligned >1 times 93.18% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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 8 files... [bam_rmdupse_core] 1362190 / 10375504 = 0.1313 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 19:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.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 19:13:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:54: 1000000 INFO @ Sun, 21 Jun 2020 19:14:00: 2000000 INFO @ Sun, 21 Jun 2020 19:14:06: 3000000 INFO @ Sun, 21 Jun 2020 19:14:12: 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 19:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.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 19:14:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:18: 5000000 INFO @ Sun, 21 Jun 2020 19:14:25: 1000000 INFO @ Sun, 21 Jun 2020 19:14:25: 6000000 INFO @ Sun, 21 Jun 2020 19:14:32: 2000000 INFO @ Sun, 21 Jun 2020 19:14:32: 7000000 INFO @ Sun, 21 Jun 2020 19:14:39: 3000000 INFO @ Sun, 21 Jun 2020 19:14:39: 8000000 INFO @ Sun, 21 Jun 2020 19:14:45: 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 19:14:46: 9000000 INFO @ Sun, 21 Jun 2020 19:14:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:47: #1 total tags in treatment: 9013314 INFO @ Sun, 21 Jun 2020 19:14:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:47: #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 19:14:47: #1 tags after filtering in treatment: 9013313 INFO @ Sun, 21 Jun 2020 19:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.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 19:14:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:48: #2 number of paired peaks: 637 WARNING @ Sun, 21 Jun 2020 19:14:48: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:48: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 19:14:48: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 19:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.05_model.r INFO @ Sun, 21 Jun 2020 19:14:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:53: 5000000 INFO @ Sun, 21 Jun 2020 19:14:56: 1000000 INFO @ Sun, 21 Jun 2020 19:15:00: 6000000 INFO @ Sun, 21 Jun 2020 19:15:05: 2000000 INFO @ Sun, 21 Jun 2020 19:15:08: 7000000 INFO @ Sun, 21 Jun 2020 19:15:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:13: 3000000 INFO @ Sun, 21 Jun 2020 19:15:16: 8000000 INFO @ Sun, 21 Jun 2020 19:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:18: Done! pass1 - making usageList (564 chroms): 1 millis pass2 - checking and writing primary data (1696 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:22: 4000000 INFO @ Sun, 21 Jun 2020 19:15:23: 9000000 INFO @ Sun, 21 Jun 2020 19:15:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:23: #1 total tags in treatment: 9013314 INFO @ Sun, 21 Jun 2020 19:15:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:23: #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 19:15:24: #1 tags after filtering in treatment: 9013313 INFO @ Sun, 21 Jun 2020 19:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:24: #2 number of paired peaks: 637 WARNING @ Sun, 21 Jun 2020 19:15:24: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:24: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 19:15:24: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 19:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.10_model.r INFO @ Sun, 21 Jun 2020 19:15:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:30: 5000000 INFO @ Sun, 21 Jun 2020 19:15:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:46: 7000000 INFO @ Sun, 21 Jun 2020 19:15:54: 8000000 INFO @ Sun, 21 Jun 2020 19:15:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.10_summits.bed INFO @ Sun, 21 Jun 2020 19:15:55: Done! pass1 - making usageList (464 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:02: 9000000 INFO @ Sun, 21 Jun 2020 19:16:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:02: #1 total tags in treatment: 9013314 INFO @ Sun, 21 Jun 2020 19:16:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:02: #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 19:16:02: #1 tags after filtering in treatment: 9013313 INFO @ Sun, 21 Jun 2020 19:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:03: #2 number of paired peaks: 637 WARNING @ Sun, 21 Jun 2020 19:16:03: Fewer paired peaks (637) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 637 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:03: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 19:16:03: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 19:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.20_model.r INFO @ Sun, 21 Jun 2020 19:16:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287883/SRX287883.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:35: Done! pass1 - making usageList (379 chroms): 1 millis pass2 - checking and writing primary data (945 records, 4 fields): 13 millis CompletedMACS2peakCalling