Job ID = 6456921 SRX = SRX4068068 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:09:10 prefetch.2.10.7: 1) Downloading 'SRR7148579'... 2020-06-21T11:09:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:12:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:12:26 prefetch.2.10.7: 'SRR7148579' is valid 2020-06-21T11:12:26 prefetch.2.10.7: 1) 'SRR7148579' was downloaded successfully Read 10890062 spots for SRR7148579/SRR7148579.sra Written 10890062 spots for SRR7148579/SRR7148579.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: 00:02:46 10890062 reads; of these: 10890062 (100.00%) were unpaired; of these: 570504 (5.24%) aligned 0 times 8481840 (77.89%) aligned exactly 1 time 1837718 (16.88%) aligned >1 times 94.76% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 1272225 / 10319558 = 0.1233 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 20:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.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 20:18:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:03: 1000000 INFO @ Sun, 21 Jun 2020 20:19:10: 2000000 INFO @ Sun, 21 Jun 2020 20:19:16: 3000000 INFO @ Sun, 21 Jun 2020 20:19:22: 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 20:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.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 20:19:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:28: 5000000 INFO @ Sun, 21 Jun 2020 20:19:34: 1000000 INFO @ Sun, 21 Jun 2020 20:19:34: 6000000 INFO @ Sun, 21 Jun 2020 20:19:40: 2000000 INFO @ Sun, 21 Jun 2020 20:19:41: 7000000 INFO @ Sun, 21 Jun 2020 20:19:47: 3000000 INFO @ Sun, 21 Jun 2020 20:19:48: 8000000 INFO @ Sun, 21 Jun 2020 20:19:53: 4000000 INFO @ Sun, 21 Jun 2020 20:19:54: 9000000 INFO @ Sun, 21 Jun 2020 20:19:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:19:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:19:55: #1 total tags in treatment: 9047333 INFO @ Sun, 21 Jun 2020 20:19:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:55: #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 20:19:55: #1 tags after filtering in treatment: 9047307 INFO @ Sun, 21 Jun 2020 20:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:55: #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 20:19:56: #2 number of paired peaks: 2022 INFO @ Sun, 21 Jun 2020 20:19:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:56: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:56: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:56: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:56: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 20:19:56: #2 alternative fragment length(s) may be 149,596 bps INFO @ Sun, 21 Jun 2020 20:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.05_model.r INFO @ Sun, 21 Jun 2020 20:19:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.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 20:19:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:20:00: 5000000 INFO @ Sun, 21 Jun 2020 20:20:04: 1000000 INFO @ Sun, 21 Jun 2020 20:20:06: 6000000 INFO @ Sun, 21 Jun 2020 20:20:11: 2000000 INFO @ Sun, 21 Jun 2020 20:20:13: 7000000 INFO @ Sun, 21 Jun 2020 20:20:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:17: 3000000 INFO @ Sun, 21 Jun 2020 20:20:20: 8000000 INFO @ Sun, 21 Jun 2020 20:20:24: 4000000 INFO @ Sun, 21 Jun 2020 20:20:27: 9000000 INFO @ Sun, 21 Jun 2020 20:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.05_summits.bed INFO @ Sun, 21 Jun 2020 20:20:27: Done! INFO @ Sun, 21 Jun 2020 20:20:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:27: #1 total tags in treatment: 9047333 INFO @ Sun, 21 Jun 2020 20:20:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (389 chroms): 2 millis pass2 - checking and writing primary data (6289 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:20:28: #1 tags after filtering in treatment: 9047307 INFO @ Sun, 21 Jun 2020 20:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:28: #2 number of paired peaks: 2022 INFO @ Sun, 21 Jun 2020 20:20:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:28: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 20:20:28: #2 alternative fragment length(s) may be 149,596 bps INFO @ Sun, 21 Jun 2020 20:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.10_model.r INFO @ Sun, 21 Jun 2020 20:20:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:20:30: 5000000 INFO @ Sun, 21 Jun 2020 20:20:36: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:20:43: 7000000 INFO @ Sun, 21 Jun 2020 20:20:49: 8000000 INFO @ Sun, 21 Jun 2020 20:20:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:56: 9000000 INFO @ Sun, 21 Jun 2020 20:20:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:56: #1 total tags in treatment: 9047333 INFO @ Sun, 21 Jun 2020 20:20:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:56: #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 20:20:57: #1 tags after filtering in treatment: 9047307 INFO @ Sun, 21 Jun 2020 20:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:57: #2 number of paired peaks: 2022 INFO @ Sun, 21 Jun 2020 20:20:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:57: #2 predicted fragment length is 149 bps INFO @ Sun, 21 Jun 2020 20:20:57: #2 alternative fragment length(s) may be 149,596 bps INFO @ Sun, 21 Jun 2020 20:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.20_model.r INFO @ Sun, 21 Jun 2020 20:20:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.10_summits.bed INFO @ Sun, 21 Jun 2020 20:21:02: Done! pass1 - making usageList (250 chroms): 1 millis pass2 - checking and writing primary data (3278 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:21:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4068068/SRX4068068.20_summits.bed INFO @ Sun, 21 Jun 2020 20:21:30: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (1157 records, 4 fields): 5 millis CompletedMACS2peakCalling