Job ID = 6457852 SRX = SRX4801816 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:58:33 prefetch.2.10.7: 1) Downloading 'SRR7968401'... 2020-06-21T11:58:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:01:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:01:12 prefetch.2.10.7: 'SRR7968401' is valid 2020-06-21T12:01:12 prefetch.2.10.7: 1) 'SRR7968401' was downloaded successfully Read 11180850 spots for SRR7968401/SRR7968401.sra Written 11180850 spots for SRR7968401/SRR7968401.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: 00:03:43 11180850 reads; of these: 11180850 (100.00%) were unpaired; of these: 384309 (3.44%) aligned 0 times 7624019 (68.19%) aligned exactly 1 time 3172522 (28.37%) aligned >1 times 96.56% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 2428902 / 10796541 = 0.2250 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 21:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.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 21:08:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:09:01: 1000000 INFO @ Sun, 21 Jun 2020 21:09:07: 2000000 INFO @ Sun, 21 Jun 2020 21:09:14: 3000000 INFO @ Sun, 21 Jun 2020 21:09:21: 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 21:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.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 21:09:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:09:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:09:28: 5000000 INFO @ Sun, 21 Jun 2020 21:09:32: 1000000 INFO @ Sun, 21 Jun 2020 21:09:36: 6000000 INFO @ Sun, 21 Jun 2020 21:09:39: 2000000 INFO @ Sun, 21 Jun 2020 21:09:44: 7000000 INFO @ Sun, 21 Jun 2020 21:09:47: 3000000 INFO @ Sun, 21 Jun 2020 21:09:51: 8000000 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 21:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.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 21:09:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:09:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:09:54: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:09:54: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:09:54: #1 total tags in treatment: 8367639 INFO @ Sun, 21 Jun 2020 21:09:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:54: #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 21:09:55: 4000000 INFO @ Sun, 21 Jun 2020 21:09:55: #1 tags after filtering in treatment: 8367487 INFO @ Sun, 21 Jun 2020 21:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:56: #2 number of paired peaks: 5033 INFO @ Sun, 21 Jun 2020 21:09:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:56: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:09:56: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:09:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.05_model.r INFO @ Sun, 21 Jun 2020 21:09:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:10:02: 1000000 INFO @ Sun, 21 Jun 2020 21:10:02: 5000000 INFO @ Sun, 21 Jun 2020 21:10:10: 2000000 INFO @ Sun, 21 Jun 2020 21:10:10: 6000000 INFO @ Sun, 21 Jun 2020 21:10:18: 3000000 INFO @ Sun, 21 Jun 2020 21:10:18: 7000000 INFO @ Sun, 21 Jun 2020 21:10:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:26: 4000000 INFO @ Sun, 21 Jun 2020 21:10:26: 8000000 INFO @ Sun, 21 Jun 2020 21:10:30: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:10:30: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:10:30: #1 total tags in treatment: 8367639 INFO @ Sun, 21 Jun 2020 21:10:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:10:30: #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 21:10:30: #1 tags after filtering in treatment: 8367487 INFO @ Sun, 21 Jun 2020 21:10:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:31: #2 number of paired peaks: 5033 INFO @ Sun, 21 Jun 2020 21:10:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:31: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:10:31: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.10_model.r INFO @ Sun, 21 Jun 2020 21:10:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:10:33: 5000000 INFO @ Sun, 21 Jun 2020 21:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.05_summits.bed INFO @ Sun, 21 Jun 2020 21:10:35: Done! pass1 - making usageList (530 chroms): 2 millis pass2 - checking and writing primary data (8461 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:10:40: 6000000 INFO @ Sun, 21 Jun 2020 21:10:48: 7000000 INFO @ Sun, 21 Jun 2020 21:10:55: 8000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:10:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:58: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:10:58: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:10:58: #1 total tags in treatment: 8367639 INFO @ Sun, 21 Jun 2020 21:10:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:10:58: #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 21:10:58: #1 tags after filtering in treatment: 8367487 INFO @ Sun, 21 Jun 2020 21:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:59: #2 number of paired peaks: 5033 INFO @ Sun, 21 Jun 2020 21:10:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:59: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:10:59: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.20_model.r INFO @ Sun, 21 Jun 2020 21:10:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.10_summits.bed INFO @ Sun, 21 Jun 2020 21:11:09: Done! pass1 - making usageList (424 chroms): 1 millis pass2 - checking and writing primary data (6957 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:11:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801816/SRX4801816.20_summits.bed INFO @ Sun, 21 Jun 2020 21:11:37: Done! pass1 - making usageList (251 chroms): 2 millis pass2 - checking and writing primary data (5102 records, 4 fields): 13 millis CompletedMACS2peakCalling