Job ID = 6498727 SRX = SRX749050 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:59:34 prefetch.2.10.7: 1) Downloading 'SRR1636778'... 2020-06-25T23:59:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:03:09 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:03:09 prefetch.2.10.7: 1) 'SRR1636778' was downloaded successfully Read 15617800 spots for SRR1636778/SRR1636778.sra Written 15617800 spots for SRR1636778/SRR1636778.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: 00:26:05 15617800 reads; of these: 15617800 (100.00%) were paired; of these: 1495626 (9.58%) aligned concordantly 0 times 10930112 (69.98%) aligned concordantly exactly 1 time 3192062 (20.44%) aligned concordantly >1 times ---- 1495626 pairs aligned concordantly 0 times; of these: 174010 (11.63%) aligned discordantly 1 time ---- 1321616 pairs aligned 0 times concordantly or discordantly; of these: 2643232 mates make up the pairs; of these: 1943297 (73.52%) aligned 0 times 452079 (17.10%) aligned exactly 1 time 247856 (9.38%) aligned >1 times 93.78% overall alignment rate Time searching: 00:26:05 Overall time: 00:26:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 746101 / 14273834 = 0.0523 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 @ Fri, 26 Jun 2020 09:39:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.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 @ Fri, 26 Jun 2020 09:39:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:39:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:39:18: 1000000 INFO @ Fri, 26 Jun 2020 09:39:23: 2000000 INFO @ Fri, 26 Jun 2020 09:39:28: 3000000 INFO @ Fri, 26 Jun 2020 09:39:33: 4000000 INFO @ Fri, 26 Jun 2020 09:39:38: 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 @ Fri, 26 Jun 2020 09:39:43: 6000000 INFO @ Fri, 26 Jun 2020 09:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.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 @ Fri, 26 Jun 2020 09:39:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:39:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:39:48: 7000000 INFO @ Fri, 26 Jun 2020 09:39:48: 1000000 INFO @ Fri, 26 Jun 2020 09:39:53: 8000000 INFO @ Fri, 26 Jun 2020 09:39:53: 2000000 INFO @ Fri, 26 Jun 2020 09:39:58: 9000000 INFO @ Fri, 26 Jun 2020 09:39:59: 3000000 INFO @ Fri, 26 Jun 2020 09:40:03: 10000000 INFO @ Fri, 26 Jun 2020 09:40:04: 4000000 INFO @ Fri, 26 Jun 2020 09:40:08: 11000000 INFO @ Fri, 26 Jun 2020 09:40:09: 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 @ Fri, 26 Jun 2020 09:40:13: 12000000 INFO @ Fri, 26 Jun 2020 09:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.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 @ Fri, 26 Jun 2020 09:40:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:40:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:40:14: 6000000 INFO @ Fri, 26 Jun 2020 09:40:18: 13000000 INFO @ Fri, 26 Jun 2020 09:40:19: 7000000 INFO @ Fri, 26 Jun 2020 09:40:19: 1000000 INFO @ Fri, 26 Jun 2020 09:40:23: 14000000 INFO @ Fri, 26 Jun 2020 09:40:24: 8000000 INFO @ Fri, 26 Jun 2020 09:40:25: 2000000 INFO @ Fri, 26 Jun 2020 09:40:28: 15000000 INFO @ Fri, 26 Jun 2020 09:40:30: 9000000 INFO @ Fri, 26 Jun 2020 09:40:30: 3000000 INFO @ Fri, 26 Jun 2020 09:40:34: 16000000 INFO @ Fri, 26 Jun 2020 09:40:35: 10000000 INFO @ Fri, 26 Jun 2020 09:40:35: 4000000 INFO @ Fri, 26 Jun 2020 09:40:39: 17000000 INFO @ Fri, 26 Jun 2020 09:40:41: 11000000 INFO @ Fri, 26 Jun 2020 09:40:41: 5000000 INFO @ Fri, 26 Jun 2020 09:40:44: 18000000 INFO @ Fri, 26 Jun 2020 09:40:46: 12000000 INFO @ Fri, 26 Jun 2020 09:40:46: 6000000 INFO @ Fri, 26 Jun 2020 09:40:49: 19000000 INFO @ Fri, 26 Jun 2020 09:40:51: 13000000 INFO @ Fri, 26 Jun 2020 09:40:51: 7000000 INFO @ Fri, 26 Jun 2020 09:40:54: 20000000 INFO @ Fri, 26 Jun 2020 09:40:57: 14000000 INFO @ Fri, 26 Jun 2020 09:40:57: 8000000 INFO @ Fri, 26 Jun 2020 09:40:59: 21000000 INFO @ Fri, 26 Jun 2020 09:41:02: 15000000 INFO @ Fri, 26 Jun 2020 09:41:02: 9000000 INFO @ Fri, 26 Jun 2020 09:41:04: 22000000 INFO @ Fri, 26 Jun 2020 09:41:07: 16000000 INFO @ Fri, 26 Jun 2020 09:41:07: 10000000 INFO @ Fri, 26 Jun 2020 09:41:09: 23000000 INFO @ Fri, 26 Jun 2020 09:41:12: 17000000 INFO @ Fri, 26 Jun 2020 09:41:13: 11000000 INFO @ Fri, 26 Jun 2020 09:41:14: 24000000 INFO @ Fri, 26 Jun 2020 09:41:18: 18000000 INFO @ Fri, 26 Jun 2020 09:41:18: 12000000 INFO @ Fri, 26 Jun 2020 09:41:19: 25000000 INFO @ Fri, 26 Jun 2020 09:41:23: 19000000 INFO @ Fri, 26 Jun 2020 09:41:23: 13000000 INFO @ Fri, 26 Jun 2020 09:41:25: 26000000 INFO @ Fri, 26 Jun 2020 09:41:28: 20000000 INFO @ Fri, 26 Jun 2020 09:41:29: 14000000 INFO @ Fri, 26 Jun 2020 09:41:30: 27000000 INFO @ Fri, 26 Jun 2020 09:41:34: 21000000 INFO @ Fri, 26 Jun 2020 09:41:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:41:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:41:34: #1 total tags in treatment: 13377798 INFO @ Fri, 26 Jun 2020 09:41:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:41:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:41:34: 15000000 INFO @ Fri, 26 Jun 2020 09:41:34: #1 tags after filtering in treatment: 11257969 INFO @ Fri, 26 Jun 2020 09:41:34: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 09:41:34: #1 finished! INFO @ Fri, 26 Jun 2020 09:41:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:41:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:41:36: #2 number of paired peaks: 9457 INFO @ Fri, 26 Jun 2020 09:41:36: start model_add_line... INFO @ Fri, 26 Jun 2020 09:41:36: start X-correlation... INFO @ Fri, 26 Jun 2020 09:41:36: end of X-cor INFO @ Fri, 26 Jun 2020 09:41:36: #2 finished! INFO @ Fri, 26 Jun 2020 09:41:36: #2 predicted fragment length is 190 bps INFO @ Fri, 26 Jun 2020 09:41:36: #2 alternative fragment length(s) may be 190 bps INFO @ Fri, 26 Jun 2020 09:41:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.05_model.r INFO @ Fri, 26 Jun 2020 09:41:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:41:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:41:39: 22000000 INFO @ Fri, 26 Jun 2020 09:41:39: 16000000 INFO @ Fri, 26 Jun 2020 09:41:44: 23000000 INFO @ Fri, 26 Jun 2020 09:41:45: 17000000 INFO @ Fri, 26 Jun 2020 09:41:50: 24000000 INFO @ Fri, 26 Jun 2020 09:41:50: 18000000 INFO @ Fri, 26 Jun 2020 09:41:55: 25000000 INFO @ Fri, 26 Jun 2020 09:41:55: 19000000 INFO @ Fri, 26 Jun 2020 09:42:00: 26000000 INFO @ Fri, 26 Jun 2020 09:42:00: 20000000 INFO @ Fri, 26 Jun 2020 09:42:06: 27000000 INFO @ Fri, 26 Jun 2020 09:42:06: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:42:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:42:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:42:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:42:10: #1 total tags in treatment: 13377798 INFO @ Fri, 26 Jun 2020 09:42:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:42:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:42:10: #1 tags after filtering in treatment: 11257969 INFO @ Fri, 26 Jun 2020 09:42:10: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 09:42:10: #1 finished! INFO @ Fri, 26 Jun 2020 09:42:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:42:11: 22000000 INFO @ Fri, 26 Jun 2020 09:42:12: #2 number of paired peaks: 9457 INFO @ Fri, 26 Jun 2020 09:42:12: start model_add_line... INFO @ Fri, 26 Jun 2020 09:42:12: start X-correlation... INFO @ Fri, 26 Jun 2020 09:42:12: end of X-cor INFO @ Fri, 26 Jun 2020 09:42:12: #2 finished! INFO @ Fri, 26 Jun 2020 09:42:12: #2 predicted fragment length is 190 bps INFO @ Fri, 26 Jun 2020 09:42:12: #2 alternative fragment length(s) may be 190 bps INFO @ Fri, 26 Jun 2020 09:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.10_model.r INFO @ Fri, 26 Jun 2020 09:42:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:42:16: 23000000 INFO @ Fri, 26 Jun 2020 09:42:20: 24000000 INFO @ Fri, 26 Jun 2020 09:42:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:42:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:42:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.05_summits.bed INFO @ Fri, 26 Jun 2020 09:42:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8819 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:42:25: 25000000 INFO @ Fri, 26 Jun 2020 09:42:30: 26000000 INFO @ Fri, 26 Jun 2020 09:42:35: 27000000 INFO @ Fri, 26 Jun 2020 09:42:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:42:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:42:38: #1 total tags in treatment: 13377798 INFO @ Fri, 26 Jun 2020 09:42:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:42:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:42:39: #1 tags after filtering in treatment: 11257969 INFO @ Fri, 26 Jun 2020 09:42:39: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 09:42:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:42:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:42:40: #2 number of paired peaks: 9457 INFO @ Fri, 26 Jun 2020 09:42:40: start model_add_line... INFO @ Fri, 26 Jun 2020 09:42:40: start X-correlation... INFO @ Fri, 26 Jun 2020 09:42:40: end of X-cor INFO @ Fri, 26 Jun 2020 09:42:40: #2 finished! INFO @ Fri, 26 Jun 2020 09:42:40: #2 predicted fragment length is 190 bps INFO @ Fri, 26 Jun 2020 09:42:40: #2 alternative fragment length(s) may be 190 bps INFO @ Fri, 26 Jun 2020 09:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.20_model.r INFO @ Fri, 26 Jun 2020 09:42:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:42:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.10_summits.bed INFO @ Fri, 26 Jun 2020 09:42:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8000 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:43:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:43:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:43:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:43:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749050/SRX749050.20_summits.bed INFO @ Fri, 26 Jun 2020 09:43:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6788 records, 4 fields): 8 millis CompletedMACS2peakCalling