Job ID = 6454077 SRX = SRX181423 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:34 prefetch.2.10.7: 1) Downloading 'SRR548160'... 2020-06-21T09:02:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:59 prefetch.2.10.7: 'SRR548160' is valid 2020-06-21T09:03:59 prefetch.2.10.7: 1) 'SRR548160' was downloaded successfully Read 21615065 spots for SRR548160/SRR548160.sra Written 21615065 spots for SRR548160/SRR548160.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: 00:03:39 21615065 reads; of these: 21615065 (100.00%) were unpaired; of these: 2949360 (13.64%) aligned 0 times 16551062 (76.57%) aligned exactly 1 time 2114643 (9.78%) aligned >1 times 86.36% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 7939106 / 18665705 = 0.4253 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 18:11:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.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 18:11:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:01: 1000000 INFO @ Sun, 21 Jun 2020 18:12:06: 2000000 INFO @ Sun, 21 Jun 2020 18:12:11: 3000000 INFO @ Sun, 21 Jun 2020 18:12:16: 4000000 INFO @ Sun, 21 Jun 2020 18:12:20: 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 18:12:25: 6000000 INFO @ Sun, 21 Jun 2020 18:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.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 18:12:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:30: 7000000 INFO @ Sun, 21 Jun 2020 18:12:32: 1000000 INFO @ Sun, 21 Jun 2020 18:12:35: 8000000 INFO @ Sun, 21 Jun 2020 18:12:37: 2000000 INFO @ Sun, 21 Jun 2020 18:12:40: 9000000 INFO @ Sun, 21 Jun 2020 18:12:42: 3000000 INFO @ Sun, 21 Jun 2020 18:12:45: 10000000 INFO @ Sun, 21 Jun 2020 18:12:47: 4000000 INFO @ Sun, 21 Jun 2020 18:12:49: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:12:49: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:12:49: #1 total tags in treatment: 10726599 INFO @ Sun, 21 Jun 2020 18:12:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:49: #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 18:12:49: #1 tags after filtering in treatment: 10726586 INFO @ Sun, 21 Jun 2020 18:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:50: #2 number of paired peaks: 994 WARNING @ Sun, 21 Jun 2020 18:12:50: Fewer paired peaks (994) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 994 pairs to build model! INFO @ Sun, 21 Jun 2020 18:12:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:50: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:12:50: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 18:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.05_model.r INFO @ Sun, 21 Jun 2020 18:12:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:52: 5000000 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 18:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.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 18:12:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:57: 6000000 INFO @ Sun, 21 Jun 2020 18:13:02: 1000000 INFO @ Sun, 21 Jun 2020 18:13:02: 7000000 INFO @ Sun, 21 Jun 2020 18:13:07: 8000000 INFO @ Sun, 21 Jun 2020 18:13:07: 2000000 INFO @ Sun, 21 Jun 2020 18:13:12: 3000000 INFO @ Sun, 21 Jun 2020 18:13:12: 9000000 INFO @ Sun, 21 Jun 2020 18:13:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:17: 4000000 INFO @ Sun, 21 Jun 2020 18:13:17: 10000000 INFO @ Sun, 21 Jun 2020 18:13:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:13:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:13:21: #1 total tags in treatment: 10726599 INFO @ Sun, 21 Jun 2020 18:13:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:21: #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 18:13:21: #1 tags after filtering in treatment: 10726586 INFO @ Sun, 21 Jun 2020 18:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:22: 5000000 INFO @ Sun, 21 Jun 2020 18:13:22: #2 number of paired peaks: 994 WARNING @ Sun, 21 Jun 2020 18:13:22: Fewer paired peaks (994) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 994 pairs to build model! INFO @ Sun, 21 Jun 2020 18:13:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:22: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:13:22: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 18:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.10_model.r INFO @ Sun, 21 Jun 2020 18:13:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.05_summits.bed INFO @ Sun, 21 Jun 2020 18:13:25: Done! pass1 - making usageList (422 chroms): 2 millis pass2 - checking and writing primary data (7818 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:13:27: 6000000 INFO @ Sun, 21 Jun 2020 18:13:31: 7000000 INFO @ Sun, 21 Jun 2020 18:13:36: 8000000 INFO @ Sun, 21 Jun 2020 18:13:41: 9000000 INFO @ Sun, 21 Jun 2020 18:13:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:13:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:13:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:13:50: #1 total tags in treatment: 10726599 INFO @ Sun, 21 Jun 2020 18:13:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:50: #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 18:13:50: #1 tags after filtering in treatment: 10726586 INFO @ Sun, 21 Jun 2020 18:13:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:51: #2 number of paired peaks: 994 WARNING @ Sun, 21 Jun 2020 18:13:51: Fewer paired peaks (994) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 994 pairs to build model! INFO @ Sun, 21 Jun 2020 18:13:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:51: #2 predicted fragment length is 124 bps INFO @ Sun, 21 Jun 2020 18:13:51: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 21 Jun 2020 18:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.20_model.r INFO @ Sun, 21 Jun 2020 18:13:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.10_summits.bed INFO @ Sun, 21 Jun 2020 18:13:58: Done! pass1 - making usageList (323 chroms): 2 millis pass2 - checking and writing primary data (3882 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:14:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX181423/SRX181423.20_summits.bed INFO @ Sun, 21 Jun 2020 18:14:27: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (1194 records, 4 fields): 7 millis CompletedMACS2peakCalling