Job ID = 6456031 SRX = SRX3159488 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:27:36 prefetch.2.10.7: 1) Downloading 'SRR6004218'... 2020-06-21T10:27:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:40 prefetch.2.10.7: 'SRR6004218' is valid 2020-06-21T10:29:40 prefetch.2.10.7: 1) 'SRR6004218' was downloaded successfully 2020-06-21T10:29:40 prefetch.2.10.7: 'SRR6004218' has 0 unresolved dependencies Read 16231733 spots for SRR6004218/SRR6004218.sra Written 16231733 spots for SRR6004218/SRR6004218.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: 00:03:20 16231733 reads; of these: 16231733 (100.00%) were unpaired; of these: 2383979 (14.69%) aligned 0 times 11976265 (73.78%) aligned exactly 1 time 1871489 (11.53%) aligned >1 times 85.31% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 3229819 / 13847754 = 0.2332 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 19:36:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.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 19:36:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:51: 1000000 INFO @ Sun, 21 Jun 2020 19:36:56: 2000000 INFO @ Sun, 21 Jun 2020 19:37:01: 3000000 INFO @ Sun, 21 Jun 2020 19:37:06: 4000000 INFO @ Sun, 21 Jun 2020 19:37:11: 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 19:37:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.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 19:37:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:17: 6000000 INFO @ Sun, 21 Jun 2020 19:37:21: 1000000 INFO @ Sun, 21 Jun 2020 19:37:22: 7000000 INFO @ Sun, 21 Jun 2020 19:37:26: 2000000 INFO @ Sun, 21 Jun 2020 19:37:28: 8000000 INFO @ Sun, 21 Jun 2020 19:37:32: 3000000 INFO @ Sun, 21 Jun 2020 19:37:34: 9000000 INFO @ Sun, 21 Jun 2020 19:37:37: 4000000 INFO @ Sun, 21 Jun 2020 19:37:39: 10000000 INFO @ Sun, 21 Jun 2020 19:37:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:37:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:37:43: #1 total tags in treatment: 10617935 INFO @ Sun, 21 Jun 2020 19:37:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:43: #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 19:37:43: 5000000 INFO @ Sun, 21 Jun 2020 19:37:43: #1 tags after filtering in treatment: 10617924 INFO @ Sun, 21 Jun 2020 19:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:43: #2 looking for paired plus/minus strand peaks... 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 19:37:44: #2 number of paired peaks: 4896 INFO @ Sun, 21 Jun 2020 19:37:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:44: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:37:44: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.05_model.r INFO @ Sun, 21 Jun 2020 19:37:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.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 19:37:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:48: 6000000 INFO @ Sun, 21 Jun 2020 19:37:51: 1000000 INFO @ Sun, 21 Jun 2020 19:37:54: 7000000 INFO @ Sun, 21 Jun 2020 19:37:56: 2000000 INFO @ Sun, 21 Jun 2020 19:37:59: 8000000 INFO @ Sun, 21 Jun 2020 19:38:02: 3000000 INFO @ Sun, 21 Jun 2020 19:38:05: 9000000 INFO @ Sun, 21 Jun 2020 19:38:07: 4000000 INFO @ Sun, 21 Jun 2020 19:38:10: 10000000 INFO @ Sun, 21 Jun 2020 19:38:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:13: 5000000 INFO @ Sun, 21 Jun 2020 19:38:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:14: #1 total tags in treatment: 10617935 INFO @ Sun, 21 Jun 2020 19:38:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:14: #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 19:38:14: #1 tags after filtering in treatment: 10617924 INFO @ Sun, 21 Jun 2020 19:38:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:16: #2 number of paired peaks: 4896 INFO @ Sun, 21 Jun 2020 19:38:16: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:16: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:16: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:16: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:16: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:38:16: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.10_model.r INFO @ Sun, 21 Jun 2020 19:38:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:18: 6000000 INFO @ Sun, 21 Jun 2020 19:38:23: 7000000 INFO @ Sun, 21 Jun 2020 19:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:25: Done! pass1 - making usageList (291 chroms): 2 millis pass2 - checking and writing primary data (7772 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:29: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:38:34: 9000000 INFO @ Sun, 21 Jun 2020 19:38:39: 10000000 INFO @ Sun, 21 Jun 2020 19:38:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:38:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:38:43: #1 total tags in treatment: 10617935 INFO @ Sun, 21 Jun 2020 19:38:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:43: #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 19:38:43: #1 tags after filtering in treatment: 10617924 INFO @ Sun, 21 Jun 2020 19:38:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:44: #2 number of paired peaks: 4896 INFO @ Sun, 21 Jun 2020 19:38:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:45: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:38:45: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.20_model.r INFO @ Sun, 21 Jun 2020 19:38:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:54: Done! pass1 - making usageList (149 chroms): 1 millis pass2 - checking and writing primary data (6350 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159488/SRX3159488.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:23: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (4820 records, 4 fields): 8 millis CompletedMACS2peakCalling