Job ID = 6457864 SRX = SRX481130 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:02:17 prefetch.2.10.7: 1) Downloading 'SRR1182753'... 2020-06-21T12:02:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:07:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:07:02 prefetch.2.10.7: 1) 'SRR1182753' was downloaded successfully Read 22423058 spots for SRR1182753/SRR1182753.sra Written 22423058 spots for SRR1182753/SRR1182753.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: 00:05:41 22423058 reads; of these: 22423058 (100.00%) were unpaired; of these: 1290249 (5.75%) aligned 0 times 17883512 (79.76%) aligned exactly 1 time 3249297 (14.49%) aligned >1 times 94.25% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 2472530 / 21132809 = 0.1170 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 21:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.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 21:19:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:46: 1000000 INFO @ Sun, 21 Jun 2020 21:19:52: 2000000 INFO @ Sun, 21 Jun 2020 21:19:58: 3000000 INFO @ Sun, 21 Jun 2020 21:20:05: 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 21:20:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.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 21:20:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:11: 5000000 INFO @ Sun, 21 Jun 2020 21:20:16: 1000000 INFO @ Sun, 21 Jun 2020 21:20:18: 6000000 INFO @ Sun, 21 Jun 2020 21:20:23: 2000000 INFO @ Sun, 21 Jun 2020 21:20:24: 7000000 INFO @ Sun, 21 Jun 2020 21:20:30: 3000000 INFO @ Sun, 21 Jun 2020 21:20:31: 8000000 INFO @ Sun, 21 Jun 2020 21:20:37: 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 21:20:38: 9000000 INFO @ Sun, 21 Jun 2020 21:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.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 21:20:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:44: 5000000 INFO @ Sun, 21 Jun 2020 21:20:45: 10000000 INFO @ Sun, 21 Jun 2020 21:20:46: 1000000 INFO @ Sun, 21 Jun 2020 21:20:51: 6000000 INFO @ Sun, 21 Jun 2020 21:20:52: 11000000 INFO @ Sun, 21 Jun 2020 21:20:53: 2000000 INFO @ Sun, 21 Jun 2020 21:20:58: 7000000 INFO @ Sun, 21 Jun 2020 21:20:58: 12000000 INFO @ Sun, 21 Jun 2020 21:21:00: 3000000 INFO @ Sun, 21 Jun 2020 21:21:05: 8000000 INFO @ Sun, 21 Jun 2020 21:21:05: 13000000 INFO @ Sun, 21 Jun 2020 21:21:07: 4000000 INFO @ Sun, 21 Jun 2020 21:21:11: 9000000 INFO @ Sun, 21 Jun 2020 21:21:12: 14000000 INFO @ Sun, 21 Jun 2020 21:21:14: 5000000 INFO @ Sun, 21 Jun 2020 21:21:18: 10000000 INFO @ Sun, 21 Jun 2020 21:21:19: 15000000 INFO @ Sun, 21 Jun 2020 21:21:20: 6000000 INFO @ Sun, 21 Jun 2020 21:21:25: 11000000 INFO @ Sun, 21 Jun 2020 21:21:26: 16000000 INFO @ Sun, 21 Jun 2020 21:21:27: 7000000 INFO @ Sun, 21 Jun 2020 21:21:31: 12000000 INFO @ Sun, 21 Jun 2020 21:21:33: 17000000 INFO @ Sun, 21 Jun 2020 21:21:34: 8000000 INFO @ Sun, 21 Jun 2020 21:21:38: 13000000 INFO @ Sun, 21 Jun 2020 21:21:40: 18000000 INFO @ Sun, 21 Jun 2020 21:21:41: 9000000 INFO @ Sun, 21 Jun 2020 21:21:44: 14000000 INFO @ Sun, 21 Jun 2020 21:21:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:45: #1 total tags in treatment: 18660279 INFO @ Sun, 21 Jun 2020 21:21:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:45: #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 21:21:45: #1 tags after filtering in treatment: 18660278 INFO @ Sun, 21 Jun 2020 21:21:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:47: #2 number of paired peaks: 342 WARNING @ Sun, 21 Jun 2020 21:21:47: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Sun, 21 Jun 2020 21:21:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:47: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:21:47: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.05_model.r INFO @ Sun, 21 Jun 2020 21:21:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:47: 10000000 INFO @ Sun, 21 Jun 2020 21:21:51: 15000000 INFO @ Sun, 21 Jun 2020 21:21:54: 11000000 INFO @ Sun, 21 Jun 2020 21:21:58: 16000000 INFO @ Sun, 21 Jun 2020 21:22:00: 12000000 INFO @ Sun, 21 Jun 2020 21:22:05: 17000000 INFO @ Sun, 21 Jun 2020 21:22:06: 13000000 INFO @ Sun, 21 Jun 2020 21:22:11: 18000000 INFO @ Sun, 21 Jun 2020 21:22:13: 14000000 INFO @ Sun, 21 Jun 2020 21:22:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:16: #1 total tags in treatment: 18660279 INFO @ Sun, 21 Jun 2020 21:22:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:16: #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 21:22:17: #1 tags after filtering in treatment: 18660278 INFO @ Sun, 21 Jun 2020 21:22:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:18: #2 number of paired peaks: 342 WARNING @ Sun, 21 Jun 2020 21:22:18: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Sun, 21 Jun 2020 21:22:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:18: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:22:18: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.10_model.r INFO @ Sun, 21 Jun 2020 21:22:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:19: 15000000 INFO @ Sun, 21 Jun 2020 21:22:26: 16000000 INFO @ Sun, 21 Jun 2020 21:22:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:32: 17000000 INFO @ Sun, 21 Jun 2020 21:22:38: 18000000 INFO @ Sun, 21 Jun 2020 21:22:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:22:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:22:42: #1 total tags in treatment: 18660279 INFO @ Sun, 21 Jun 2020 21:22:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:42: #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 21:22:43: #1 tags after filtering in treatment: 18660278 INFO @ Sun, 21 Jun 2020 21:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:44: #2 number of paired peaks: 342 WARNING @ Sun, 21 Jun 2020 21:22:44: Fewer paired peaks (342) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 342 pairs to build model! INFO @ Sun, 21 Jun 2020 21:22:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:44: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:22:44: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:22:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.20_model.r INFO @ Sun, 21 Jun 2020 21:22:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.05_summits.bed INFO @ Sun, 21 Jun 2020 21:22:51: Done! pass1 - making usageList (367 chroms): 2 millis pass2 - checking and writing primary data (6073 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.10_summits.bed INFO @ Sun, 21 Jun 2020 21:23:23: Done! pass1 - making usageList (211 chroms): 2 millis pass2 - checking and writing primary data (4292 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481130/SRX481130.20_summits.bed INFO @ Sun, 21 Jun 2020 21:23:50: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (2605 records, 4 fields): 7 millis CompletedMACS2peakCalling