Job ID = 6452910 SRX = SRX042250 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:48:15 prefetch.2.10.7: 1) Downloading 'SRR100231'... 2020-06-21T07:48:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:02:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:02:51 prefetch.2.10.7: 1) 'SRR100231' was downloaded successfully Read 33324254 spots for SRR100231/SRR100231.sra Written 33324254 spots for SRR100231/SRR100231.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: 00:12:13 33324254 reads; of these: 33324254 (100.00%) were unpaired; of these: 8419915 (25.27%) aligned 0 times 20703432 (62.13%) aligned exactly 1 time 4200907 (12.61%) aligned >1 times 74.73% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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 12 files... [bam_rmdupse_core] 8811824 / 24904339 = 0.3538 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 17:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.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 17:27:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:12: 1000000 INFO @ Sun, 21 Jun 2020 17:27:23: 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 @ Sun, 21 Jun 2020 17:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.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 17:27:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:34: 3000000 INFO @ Sun, 21 Jun 2020 17:27:41: 1000000 INFO @ Sun, 21 Jun 2020 17:27:45: 4000000 INFO @ Sun, 21 Jun 2020 17:27:50: 2000000 INFO @ Sun, 21 Jun 2020 17:27:56: 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 17:27:59: 3000000 INFO @ Sun, 21 Jun 2020 17:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.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 17:28:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:07: 6000000 INFO @ Sun, 21 Jun 2020 17:28:08: 4000000 INFO @ Sun, 21 Jun 2020 17:28:10: 1000000 INFO @ Sun, 21 Jun 2020 17:28:17: 5000000 INFO @ Sun, 21 Jun 2020 17:28:17: 7000000 INFO @ Sun, 21 Jun 2020 17:28:20: 2000000 INFO @ Sun, 21 Jun 2020 17:28:26: 6000000 INFO @ Sun, 21 Jun 2020 17:28:28: 8000000 INFO @ Sun, 21 Jun 2020 17:28:29: 3000000 INFO @ Sun, 21 Jun 2020 17:28:35: 7000000 INFO @ Sun, 21 Jun 2020 17:28:38: 4000000 INFO @ Sun, 21 Jun 2020 17:28:39: 9000000 INFO @ Sun, 21 Jun 2020 17:28:44: 8000000 INFO @ Sun, 21 Jun 2020 17:28:47: 5000000 INFO @ Sun, 21 Jun 2020 17:28:49: 10000000 INFO @ Sun, 21 Jun 2020 17:28:53: 9000000 INFO @ Sun, 21 Jun 2020 17:28:56: 6000000 INFO @ Sun, 21 Jun 2020 17:29:00: 11000000 INFO @ Sun, 21 Jun 2020 17:29:02: 10000000 INFO @ Sun, 21 Jun 2020 17:29:05: 7000000 INFO @ Sun, 21 Jun 2020 17:29:10: 12000000 INFO @ Sun, 21 Jun 2020 17:29:11: 11000000 INFO @ Sun, 21 Jun 2020 17:29:14: 8000000 INFO @ Sun, 21 Jun 2020 17:29:20: 13000000 INFO @ Sun, 21 Jun 2020 17:29:20: 12000000 INFO @ Sun, 21 Jun 2020 17:29:23: 9000000 INFO @ Sun, 21 Jun 2020 17:29:29: 13000000 INFO @ Sun, 21 Jun 2020 17:29:29: 14000000 INFO @ Sun, 21 Jun 2020 17:29:31: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:38: 15000000 INFO @ Sun, 21 Jun 2020 17:29:39: 14000000 INFO @ Sun, 21 Jun 2020 17:29:40: 11000000 INFO @ Sun, 21 Jun 2020 17:29:48: 15000000 INFO @ Sun, 21 Jun 2020 17:29:48: 16000000 INFO @ Sun, 21 Jun 2020 17:29:49: 12000000 INFO @ Sun, 21 Jun 2020 17:29:49: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:29:49: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:29:49: #1 total tags in treatment: 16092515 INFO @ Sun, 21 Jun 2020 17:29:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:49: #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 17:29:50: #1 tags after filtering in treatment: 16092494 INFO @ Sun, 21 Jun 2020 17:29:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:52: #2 number of paired peaks: 187 WARNING @ Sun, 21 Jun 2020 17:29:52: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 21 Jun 2020 17:29:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:52: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 17:29:52: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 17:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.05_model.r INFO @ Sun, 21 Jun 2020 17:29:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:57: 16000000 INFO @ Sun, 21 Jun 2020 17:29:58: 13000000 INFO @ Sun, 21 Jun 2020 17:29:58: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:29:58: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:29:58: #1 total tags in treatment: 16092515 INFO @ Sun, 21 Jun 2020 17:29:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:58: #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 17:29:59: #1 tags after filtering in treatment: 16092494 INFO @ Sun, 21 Jun 2020 17:29:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:00: #2 number of paired peaks: 187 WARNING @ Sun, 21 Jun 2020 17:30:00: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 21 Jun 2020 17:30:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:00: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 17:30:00: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 17:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.10_model.r INFO @ Sun, 21 Jun 2020 17:30:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:07: 14000000 INFO @ Sun, 21 Jun 2020 17:30:15: 15000000 INFO @ Sun, 21 Jun 2020 17:30:24: 16000000 INFO @ Sun, 21 Jun 2020 17:30:24: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:30:24: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:30:24: #1 total tags in treatment: 16092515 INFO @ Sun, 21 Jun 2020 17:30:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:30:25: #1 tags after filtering in treatment: 16092494 INFO @ Sun, 21 Jun 2020 17:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:25: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:26: #2 number of paired peaks: 187 WARNING @ Sun, 21 Jun 2020 17:30:26: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 21 Jun 2020 17:30:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:27: #2 predicted fragment length is 222 bps INFO @ Sun, 21 Jun 2020 17:30:27: #2 alternative fragment length(s) may be 222 bps INFO @ Sun, 21 Jun 2020 17:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.20_model.r INFO @ Sun, 21 Jun 2020 17:30:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.05_summits.bed INFO @ Sun, 21 Jun 2020 17:30:45: Done! pass1 - making usageList (354 chroms): 4 millis pass2 - checking and writing primary data (19185 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.10_summits.bed INFO @ Sun, 21 Jun 2020 17:30:56: Done! pass1 - making usageList (191 chroms): 3 millis pass2 - checking and writing primary data (9833 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX042250/SRX042250.20_summits.bed INFO @ Sun, 21 Jun 2020 17:31:21: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (3360 records, 4 fields): 10 millis CompletedMACS2peakCalling