Job ID = 6455808 SRX = SRX3009516 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:06 prefetch.2.10.7: 1) Downloading 'SRR5832217'... 2020-06-21T10:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:56 prefetch.2.10.7: 'SRR5832217' is valid 2020-06-21T10:19:56 prefetch.2.10.7: 1) 'SRR5832217' was downloaded successfully Read 14778996 spots for SRR5832217/SRR5832217.sra Written 14778996 spots for SRR5832217/SRR5832217.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: 00:03:35 14778996 reads; of these: 14778996 (100.00%) were unpaired; of these: 4915817 (33.26%) aligned 0 times 6713326 (45.42%) aligned exactly 1 time 3149853 (21.31%) aligned >1 times 66.74% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 2419620 / 9863179 = 0.2453 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 19:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.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 19:27:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:11: 1000000 INFO @ Sun, 21 Jun 2020 19:27:17: 2000000 INFO @ Sun, 21 Jun 2020 19:27:22: 3000000 INFO @ Sun, 21 Jun 2020 19:27:27: 4000000 INFO @ Sun, 21 Jun 2020 19:27:33: 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 @ Sun, 21 Jun 2020 19:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.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 19:27:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:39: 6000000 INFO @ Sun, 21 Jun 2020 19:27:43: 1000000 INFO @ Sun, 21 Jun 2020 19:27:46: 7000000 INFO @ Sun, 21 Jun 2020 19:27:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:27:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:27:49: #1 total tags in treatment: 7443559 INFO @ Sun, 21 Jun 2020 19:27:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:49: #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 19:27:49: #1 tags after filtering in treatment: 7443385 INFO @ Sun, 21 Jun 2020 19:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:50: #2 number of paired peaks: 741 WARNING @ Sun, 21 Jun 2020 19:27:50: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:50: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 19:27:50: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 19:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.05_model.r INFO @ Sun, 21 Jun 2020 19:27:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:50: 2000000 INFO @ Sun, 21 Jun 2020 19:27:57: 3000000 INFO @ Sun, 21 Jun 2020 19:28:04: 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 19:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.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 19:28:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:11: 5000000 INFO @ Sun, 21 Jun 2020 19:28:12: 1000000 INFO @ Sun, 21 Jun 2020 19:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.05_summits.bed INFO @ Sun, 21 Jun 2020 19:28:15: Done! pass1 - making usageList (661 chroms): 2 millis pass2 - checking and writing primary data (4834 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:28:18: 6000000 INFO @ Sun, 21 Jun 2020 19:28:19: 2000000 INFO @ Sun, 21 Jun 2020 19:28:25: 7000000 INFO @ Sun, 21 Jun 2020 19:28:25: 3000000 INFO @ Sun, 21 Jun 2020 19:28:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:28:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:28:29: #1 total tags in treatment: 7443559 INFO @ Sun, 21 Jun 2020 19:28:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:29: #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 19:28:29: #1 tags after filtering in treatment: 7443385 INFO @ Sun, 21 Jun 2020 19:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:29: #2 number of paired peaks: 741 WARNING @ Sun, 21 Jun 2020 19:28:29: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:30: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 19:28:30: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 19:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.10_model.r INFO @ Sun, 21 Jun 2020 19:28:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:32: 4000000 INFO @ Sun, 21 Jun 2020 19:28:38: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:44: 6000000 INFO @ Sun, 21 Jun 2020 19:28:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:49: 7000000 INFO @ Sun, 21 Jun 2020 19:28:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:28:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:28:52: #1 total tags in treatment: 7443559 INFO @ Sun, 21 Jun 2020 19:28:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:52: #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 19:28:52: #1 tags after filtering in treatment: 7443385 INFO @ Sun, 21 Jun 2020 19:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:53: #2 number of paired peaks: 741 WARNING @ Sun, 21 Jun 2020 19:28:53: Fewer paired peaks (741) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 741 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:53: #2 predicted fragment length is 153 bps INFO @ Sun, 21 Jun 2020 19:28:53: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 21 Jun 2020 19:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.20_model.r INFO @ Sun, 21 Jun 2020 19:28:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:53: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (2013 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009516/SRX3009516.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:17: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (542 records, 4 fields): 7 millis CompletedMACS2peakCalling