Job ID = 6497813 SRX = SRX1728716 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:00:21 prefetch.2.10.7: 1) Downloading 'SRR3452733'... 2020-06-25T23:00:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:02:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:02:48 prefetch.2.10.7: 1) 'SRR3452733' was downloaded successfully 2020-06-25T23:02:48 prefetch.2.10.7: 'SRR3452733' has 0 unresolved dependencies Read 21546485 spots for SRR3452733/SRR3452733.sra Written 21546485 spots for SRR3452733/SRR3452733.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:33:21 21546485 reads; of these: 21546485 (100.00%) were paired; of these: 2699729 (12.53%) aligned concordantly 0 times 15249682 (70.78%) aligned concordantly exactly 1 time 3597074 (16.69%) aligned concordantly >1 times ---- 2699729 pairs aligned concordantly 0 times; of these: 301785 (11.18%) aligned discordantly 1 time ---- 2397944 pairs aligned 0 times concordantly or discordantly; of these: 4795888 mates make up the pairs; of these: 3645709 (76.02%) aligned 0 times 834133 (17.39%) aligned exactly 1 time 316046 (6.59%) aligned >1 times 91.54% overall alignment rate Time searching: 00:33:22 Overall time: 00:33:22 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 20 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] 3064413 / 19134572 = 0.1602 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 08:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.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 08:48:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:09: 1000000 INFO @ Fri, 26 Jun 2020 08:48:14: 2000000 INFO @ Fri, 26 Jun 2020 08:48:19: 3000000 INFO @ Fri, 26 Jun 2020 08:48:25: 4000000 INFO @ Fri, 26 Jun 2020 08:48:30: 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 08:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.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 08:48:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:36: 6000000 INFO @ Fri, 26 Jun 2020 08:48:39: 1000000 INFO @ Fri, 26 Jun 2020 08:48:42: 7000000 INFO @ Fri, 26 Jun 2020 08:48:45: 2000000 INFO @ Fri, 26 Jun 2020 08:48:48: 8000000 INFO @ Fri, 26 Jun 2020 08:48:51: 3000000 INFO @ Fri, 26 Jun 2020 08:48:53: 9000000 INFO @ Fri, 26 Jun 2020 08:48:57: 4000000 INFO @ Fri, 26 Jun 2020 08:48:59: 10000000 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 08:49:03: 5000000 INFO @ Fri, 26 Jun 2020 08:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.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 08:49:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:49:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:49:05: 11000000 INFO @ Fri, 26 Jun 2020 08:49:09: 6000000 INFO @ Fri, 26 Jun 2020 08:49:09: 1000000 INFO @ Fri, 26 Jun 2020 08:49:11: 12000000 INFO @ Fri, 26 Jun 2020 08:49:15: 2000000 INFO @ Fri, 26 Jun 2020 08:49:15: 7000000 INFO @ Fri, 26 Jun 2020 08:49:17: 13000000 INFO @ Fri, 26 Jun 2020 08:49:21: 8000000 INFO @ Fri, 26 Jun 2020 08:49:22: 3000000 INFO @ Fri, 26 Jun 2020 08:49:23: 14000000 INFO @ Fri, 26 Jun 2020 08:49:27: 9000000 INFO @ Fri, 26 Jun 2020 08:49:28: 4000000 INFO @ Fri, 26 Jun 2020 08:49:29: 15000000 INFO @ Fri, 26 Jun 2020 08:49:34: 10000000 INFO @ Fri, 26 Jun 2020 08:49:34: 5000000 INFO @ Fri, 26 Jun 2020 08:49:35: 16000000 INFO @ Fri, 26 Jun 2020 08:49:40: 11000000 INFO @ Fri, 26 Jun 2020 08:49:40: 6000000 INFO @ Fri, 26 Jun 2020 08:49:41: 17000000 INFO @ Fri, 26 Jun 2020 08:49:46: 12000000 INFO @ Fri, 26 Jun 2020 08:49:46: 7000000 INFO @ Fri, 26 Jun 2020 08:49:47: 18000000 INFO @ Fri, 26 Jun 2020 08:49:52: 13000000 INFO @ Fri, 26 Jun 2020 08:49:52: 8000000 INFO @ Fri, 26 Jun 2020 08:49:53: 19000000 INFO @ Fri, 26 Jun 2020 08:49:58: 14000000 INFO @ Fri, 26 Jun 2020 08:49:58: 9000000 INFO @ Fri, 26 Jun 2020 08:49:59: 20000000 INFO @ Fri, 26 Jun 2020 08:50:04: 15000000 INFO @ Fri, 26 Jun 2020 08:50:04: 10000000 INFO @ Fri, 26 Jun 2020 08:50:05: 21000000 INFO @ Fri, 26 Jun 2020 08:50:10: 16000000 INFO @ Fri, 26 Jun 2020 08:50:10: 11000000 INFO @ Fri, 26 Jun 2020 08:50:11: 22000000 INFO @ Fri, 26 Jun 2020 08:50:16: 17000000 INFO @ Fri, 26 Jun 2020 08:50:16: 12000000 INFO @ Fri, 26 Jun 2020 08:50:17: 23000000 INFO @ Fri, 26 Jun 2020 08:50:22: 18000000 INFO @ Fri, 26 Jun 2020 08:50:22: 13000000 INFO @ Fri, 26 Jun 2020 08:50:23: 24000000 INFO @ Fri, 26 Jun 2020 08:50:28: 19000000 INFO @ Fri, 26 Jun 2020 08:50:28: 14000000 INFO @ Fri, 26 Jun 2020 08:50:29: 25000000 INFO @ Fri, 26 Jun 2020 08:50:34: 20000000 INFO @ Fri, 26 Jun 2020 08:50:34: 15000000 INFO @ Fri, 26 Jun 2020 08:50:35: 26000000 INFO @ Fri, 26 Jun 2020 08:50:40: 21000000 INFO @ Fri, 26 Jun 2020 08:50:40: 16000000 INFO @ Fri, 26 Jun 2020 08:50:42: 27000000 INFO @ Fri, 26 Jun 2020 08:50:46: 22000000 INFO @ Fri, 26 Jun 2020 08:50:46: 17000000 INFO @ Fri, 26 Jun 2020 08:50:48: 28000000 INFO @ Fri, 26 Jun 2020 08:50:52: 23000000 INFO @ Fri, 26 Jun 2020 08:50:52: 18000000 INFO @ Fri, 26 Jun 2020 08:50:54: 29000000 INFO @ Fri, 26 Jun 2020 08:50:58: 24000000 INFO @ Fri, 26 Jun 2020 08:50:58: 19000000 INFO @ Fri, 26 Jun 2020 08:51:00: 30000000 INFO @ Fri, 26 Jun 2020 08:51:04: 25000000 INFO @ Fri, 26 Jun 2020 08:51:04: 20000000 INFO @ Fri, 26 Jun 2020 08:51:06: 31000000 INFO @ Fri, 26 Jun 2020 08:51:10: 21000000 INFO @ Fri, 26 Jun 2020 08:51:11: 26000000 INFO @ Fri, 26 Jun 2020 08:51:12: 32000000 INFO @ Fri, 26 Jun 2020 08:51:17: 22000000 INFO @ Fri, 26 Jun 2020 08:51:17: 27000000 INFO @ Fri, 26 Jun 2020 08:51:18: 33000000 INFO @ Fri, 26 Jun 2020 08:51:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:51:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:51:20: #1 total tags in treatment: 15804710 INFO @ Fri, 26 Jun 2020 08:51:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:20: #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 08:51:21: #1 tags after filtering in treatment: 10190444 INFO @ Fri, 26 Jun 2020 08:51:21: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 26 Jun 2020 08:51:21: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:22: #2 number of paired peaks: 3601 INFO @ Fri, 26 Jun 2020 08:51:22: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:22: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:22: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:22: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:22: #2 predicted fragment length is 178 bps INFO @ Fri, 26 Jun 2020 08:51:22: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 26 Jun 2020 08:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.05_model.r INFO @ Fri, 26 Jun 2020 08:51:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:51:23: 23000000 INFO @ Fri, 26 Jun 2020 08:51:23: 28000000 INFO @ Fri, 26 Jun 2020 08:51:29: 24000000 INFO @ Fri, 26 Jun 2020 08:51:29: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:51:35: 25000000 INFO @ Fri, 26 Jun 2020 08:51:35: 30000000 INFO @ Fri, 26 Jun 2020 08:51:41: 26000000 INFO @ Fri, 26 Jun 2020 08:51:41: 31000000 INFO @ Fri, 26 Jun 2020 08:51:47: 27000000 INFO @ Fri, 26 Jun 2020 08:51:47: 32000000 INFO @ Fri, 26 Jun 2020 08:51:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:51:53: 33000000 INFO @ Fri, 26 Jun 2020 08:51:54: 28000000 INFO @ Fri, 26 Jun 2020 08:51:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:51:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:51:55: #1 total tags in treatment: 15804710 INFO @ Fri, 26 Jun 2020 08:51:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:55: #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 08:51:56: #1 tags after filtering in treatment: 10190444 INFO @ Fri, 26 Jun 2020 08:51:56: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 26 Jun 2020 08:51:56: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:57: #2 number of paired peaks: 3601 INFO @ Fri, 26 Jun 2020 08:51:57: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:57: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:57: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:57: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:57: #2 predicted fragment length is 178 bps INFO @ Fri, 26 Jun 2020 08:51:57: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 26 Jun 2020 08:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.10_model.r INFO @ Fri, 26 Jun 2020 08:51:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:00: 29000000 INFO @ Fri, 26 Jun 2020 08:52:05: 30000000 INFO @ Fri, 26 Jun 2020 08:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.05_summits.bed INFO @ Fri, 26 Jun 2020 08:52:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6151 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:52:11: 31000000 INFO @ Fri, 26 Jun 2020 08:52:17: 32000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:52:22: 33000000 INFO @ Fri, 26 Jun 2020 08:52:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:52:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:52:24: #1 total tags in treatment: 15804710 INFO @ Fri, 26 Jun 2020 08:52:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:24: #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 08:52:24: #1 tags after filtering in treatment: 10190444 INFO @ Fri, 26 Jun 2020 08:52:24: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 26 Jun 2020 08:52:24: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:25: #2 number of paired peaks: 3601 INFO @ Fri, 26 Jun 2020 08:52:25: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:26: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:26: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:26: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:26: #2 predicted fragment length is 178 bps INFO @ Fri, 26 Jun 2020 08:52:26: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 26 Jun 2020 08:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.20_model.r INFO @ Fri, 26 Jun 2020 08:52:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.10_summits.bed INFO @ Fri, 26 Jun 2020 08:52:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4562 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:52:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1728716/SRX1728716.20_summits.bed INFO @ Fri, 26 Jun 2020 08:53:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3162 records, 4 fields): 6 millis CompletedMACS2peakCalling