Job ID = 6498818 SRX = SRX974394 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:26:12 prefetch.2.10.7: 1) Downloading 'SRR1947849'... 2020-06-26T00:26:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:28:31 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:28:31 prefetch.2.10.7: 1) 'SRR1947849' was downloaded successfully Read 25853500 spots for SRR1947849/SRR1947849.sra Written 25853500 spots for SRR1947849/SRR1947849.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:21 25853500 reads; of these: 25853500 (100.00%) were paired; of these: 1430980 (5.53%) aligned concordantly 0 times 20061724 (77.60%) aligned concordantly exactly 1 time 4360796 (16.87%) aligned concordantly >1 times ---- 1430980 pairs aligned concordantly 0 times; of these: 144610 (10.11%) aligned discordantly 1 time ---- 1286370 pairs aligned 0 times concordantly or discordantly; of these: 2572740 mates make up the pairs; of these: 1598364 (62.13%) aligned 0 times 726703 (28.25%) aligned exactly 1 time 247673 (9.63%) aligned >1 times 96.91% overall alignment rate Time searching: 00:27:22 Overall time: 00:27:22 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 16 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] 5593368 / 24542033 = 0.2279 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 10:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.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 10:07:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:07:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:07:20: 1000000 INFO @ Fri, 26 Jun 2020 10:07:25: 2000000 INFO @ Fri, 26 Jun 2020 10:07:29: 3000000 INFO @ Fri, 26 Jun 2020 10:07:33: 4000000 INFO @ Fri, 26 Jun 2020 10:07:37: 5000000 INFO @ Fri, 26 Jun 2020 10:07:41: 6000000 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 10:07:45: 7000000 INFO @ Fri, 26 Jun 2020 10:07:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.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 10:07:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:07:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:07:49: 8000000 INFO @ Fri, 26 Jun 2020 10:07:51: 1000000 INFO @ Fri, 26 Jun 2020 10:07:53: 9000000 INFO @ Fri, 26 Jun 2020 10:07:55: 2000000 INFO @ Fri, 26 Jun 2020 10:07:57: 10000000 INFO @ Fri, 26 Jun 2020 10:07:59: 3000000 INFO @ Fri, 26 Jun 2020 10:08:01: 11000000 INFO @ Fri, 26 Jun 2020 10:08:03: 4000000 INFO @ Fri, 26 Jun 2020 10:08:06: 12000000 INFO @ Fri, 26 Jun 2020 10:08:08: 5000000 INFO @ Fri, 26 Jun 2020 10:08:10: 13000000 INFO @ Fri, 26 Jun 2020 10:08:12: 6000000 INFO @ Fri, 26 Jun 2020 10:08:14: 14000000 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 10:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.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 10:08:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:08:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:08:16: 7000000 INFO @ Fri, 26 Jun 2020 10:08:18: 15000000 INFO @ Fri, 26 Jun 2020 10:08:21: 8000000 INFO @ Fri, 26 Jun 2020 10:08:21: 1000000 INFO @ Fri, 26 Jun 2020 10:08:22: 16000000 INFO @ Fri, 26 Jun 2020 10:08:25: 9000000 INFO @ Fri, 26 Jun 2020 10:08:25: 2000000 INFO @ Fri, 26 Jun 2020 10:08:26: 17000000 INFO @ Fri, 26 Jun 2020 10:08:29: 10000000 INFO @ Fri, 26 Jun 2020 10:08:30: 3000000 INFO @ Fri, 26 Jun 2020 10:08:30: 18000000 INFO @ Fri, 26 Jun 2020 10:08:33: 11000000 INFO @ Fri, 26 Jun 2020 10:08:35: 19000000 INFO @ Fri, 26 Jun 2020 10:08:35: 4000000 INFO @ Fri, 26 Jun 2020 10:08:38: 12000000 INFO @ Fri, 26 Jun 2020 10:08:39: 20000000 INFO @ Fri, 26 Jun 2020 10:08:40: 5000000 INFO @ Fri, 26 Jun 2020 10:08:42: 13000000 INFO @ Fri, 26 Jun 2020 10:08:43: 21000000 INFO @ Fri, 26 Jun 2020 10:08:44: 6000000 INFO @ Fri, 26 Jun 2020 10:08:46: 14000000 INFO @ Fri, 26 Jun 2020 10:08:47: 22000000 INFO @ Fri, 26 Jun 2020 10:08:49: 7000000 INFO @ Fri, 26 Jun 2020 10:08:50: 15000000 INFO @ Fri, 26 Jun 2020 10:08:51: 23000000 INFO @ Fri, 26 Jun 2020 10:08:54: 8000000 INFO @ Fri, 26 Jun 2020 10:08:55: 16000000 INFO @ Fri, 26 Jun 2020 10:08:55: 24000000 INFO @ Fri, 26 Jun 2020 10:08:58: 9000000 INFO @ Fri, 26 Jun 2020 10:08:59: 17000000 INFO @ Fri, 26 Jun 2020 10:08:59: 25000000 INFO @ Fri, 26 Jun 2020 10:09:03: 18000000 INFO @ Fri, 26 Jun 2020 10:09:03: 10000000 INFO @ Fri, 26 Jun 2020 10:09:03: 26000000 INFO @ Fri, 26 Jun 2020 10:09:07: 19000000 INFO @ Fri, 26 Jun 2020 10:09:08: 27000000 INFO @ Fri, 26 Jun 2020 10:09:08: 11000000 INFO @ Fri, 26 Jun 2020 10:09:11: 20000000 INFO @ Fri, 26 Jun 2020 10:09:12: 28000000 INFO @ Fri, 26 Jun 2020 10:09:12: 12000000 INFO @ Fri, 26 Jun 2020 10:09:15: 21000000 INFO @ Fri, 26 Jun 2020 10:09:16: 29000000 INFO @ Fri, 26 Jun 2020 10:09:17: 13000000 INFO @ Fri, 26 Jun 2020 10:09:19: 22000000 INFO @ Fri, 26 Jun 2020 10:09:20: 30000000 INFO @ Fri, 26 Jun 2020 10:09:21: 14000000 INFO @ Fri, 26 Jun 2020 10:09:23: 23000000 INFO @ Fri, 26 Jun 2020 10:09:24: 31000000 INFO @ Fri, 26 Jun 2020 10:09:26: 15000000 INFO @ Fri, 26 Jun 2020 10:09:27: 24000000 INFO @ Fri, 26 Jun 2020 10:09:28: 32000000 INFO @ Fri, 26 Jun 2020 10:09:30: 16000000 INFO @ Fri, 26 Jun 2020 10:09:32: 25000000 INFO @ Fri, 26 Jun 2020 10:09:32: 33000000 INFO @ Fri, 26 Jun 2020 10:09:35: 17000000 INFO @ Fri, 26 Jun 2020 10:09:36: 26000000 INFO @ Fri, 26 Jun 2020 10:09:36: 34000000 INFO @ Fri, 26 Jun 2020 10:09:39: 18000000 INFO @ Fri, 26 Jun 2020 10:09:40: 27000000 INFO @ Fri, 26 Jun 2020 10:09:40: 35000000 INFO @ Fri, 26 Jun 2020 10:09:44: 19000000 INFO @ Fri, 26 Jun 2020 10:09:44: 28000000 INFO @ Fri, 26 Jun 2020 10:09:44: 36000000 INFO @ Fri, 26 Jun 2020 10:09:48: 20000000 INFO @ Fri, 26 Jun 2020 10:09:48: 29000000 INFO @ Fri, 26 Jun 2020 10:09:48: 37000000 INFO @ Fri, 26 Jun 2020 10:09:52: 30000000 INFO @ Fri, 26 Jun 2020 10:09:52: 21000000 INFO @ Fri, 26 Jun 2020 10:09:53: 38000000 INFO @ Fri, 26 Jun 2020 10:09:56: 31000000 INFO @ Fri, 26 Jun 2020 10:09:56: #1 tag size is determined as 25 bps INFO @ Fri, 26 Jun 2020 10:09:56: #1 tag size = 25 INFO @ Fri, 26 Jun 2020 10:09:56: #1 total tags in treatment: 18849620 INFO @ Fri, 26 Jun 2020 10:09:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:09:56: #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 10:09:57: 22000000 INFO @ Fri, 26 Jun 2020 10:09:57: #1 tags after filtering in treatment: 14543056 INFO @ Fri, 26 Jun 2020 10:09:57: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 10:09:57: #1 finished! INFO @ Fri, 26 Jun 2020 10:09:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:09:58: #2 number of paired peaks: 119 WARNING @ Fri, 26 Jun 2020 10:09:58: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Fri, 26 Jun 2020 10:09:58: start model_add_line... INFO @ Fri, 26 Jun 2020 10:09:58: start X-correlation... INFO @ Fri, 26 Jun 2020 10:09:58: end of X-cor INFO @ Fri, 26 Jun 2020 10:09:58: #2 finished! INFO @ Fri, 26 Jun 2020 10:09:58: #2 predicted fragment length is 67 bps INFO @ Fri, 26 Jun 2020 10:09:58: #2 alternative fragment length(s) may be 67,133,541,583,597 bps INFO @ Fri, 26 Jun 2020 10:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.05_model.r INFO @ Fri, 26 Jun 2020 10:09:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:10:00: 32000000 INFO @ Fri, 26 Jun 2020 10:10:01: 23000000 INFO @ Fri, 26 Jun 2020 10:10:04: 33000000 INFO @ Fri, 26 Jun 2020 10:10:06: 24000000 INFO @ Fri, 26 Jun 2020 10:10:08: 34000000 INFO @ Fri, 26 Jun 2020 10:10:10: 25000000 INFO @ Fri, 26 Jun 2020 10:10:12: 35000000 INFO @ Fri, 26 Jun 2020 10:10:14: 26000000 INFO @ Fri, 26 Jun 2020 10:10:16: 36000000 INFO @ Fri, 26 Jun 2020 10:10:19: 27000000 INFO @ Fri, 26 Jun 2020 10:10:20: 37000000 INFO @ Fri, 26 Jun 2020 10:10:23: 28000000 INFO @ Fri, 26 Jun 2020 10:10:24: 38000000 INFO @ Fri, 26 Jun 2020 10:10:28: 29000000 INFO @ Fri, 26 Jun 2020 10:10:28: #1 tag size is determined as 25 bps INFO @ Fri, 26 Jun 2020 10:10:28: #1 tag size = 25 INFO @ Fri, 26 Jun 2020 10:10:28: #1 total tags in treatment: 18849620 INFO @ Fri, 26 Jun 2020 10:10:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:10:28: #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 10:10:29: #1 tags after filtering in treatment: 14543056 INFO @ Fri, 26 Jun 2020 10:10:29: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 10:10:29: #1 finished! INFO @ Fri, 26 Jun 2020 10:10:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:10:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:10:30: #2 number of paired peaks: 119 WARNING @ Fri, 26 Jun 2020 10:10:30: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Fri, 26 Jun 2020 10:10:30: start model_add_line... INFO @ Fri, 26 Jun 2020 10:10:30: start X-correlation... INFO @ Fri, 26 Jun 2020 10:10:30: end of X-cor INFO @ Fri, 26 Jun 2020 10:10:30: #2 finished! INFO @ Fri, 26 Jun 2020 10:10:30: #2 predicted fragment length is 67 bps INFO @ Fri, 26 Jun 2020 10:10:30: #2 alternative fragment length(s) may be 67,133,541,583,597 bps INFO @ Fri, 26 Jun 2020 10:10:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.10_model.r INFO @ Fri, 26 Jun 2020 10:10:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:10:32: 30000000 INFO @ Fri, 26 Jun 2020 10:10:36: 31000000 INFO @ Fri, 26 Jun 2020 10:10:40: 32000000 INFO @ Fri, 26 Jun 2020 10:10:45: 33000000 INFO @ Fri, 26 Jun 2020 10:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.05_summits.bed INFO @ Fri, 26 Jun 2020 10:10:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3902 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:10:49: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:10:53: 35000000 INFO @ Fri, 26 Jun 2020 10:10:58: 36000000 INFO @ Fri, 26 Jun 2020 10:11:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:11:02: 37000000 INFO @ Fri, 26 Jun 2020 10:11:06: 38000000 INFO @ Fri, 26 Jun 2020 10:11:10: #1 tag size is determined as 25 bps INFO @ Fri, 26 Jun 2020 10:11:10: #1 tag size = 25 INFO @ Fri, 26 Jun 2020 10:11:10: #1 total tags in treatment: 18849620 INFO @ Fri, 26 Jun 2020 10:11:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:11:10: #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 10:11:11: #1 tags after filtering in treatment: 14543056 INFO @ Fri, 26 Jun 2020 10:11:11: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 10:11:11: #1 finished! INFO @ Fri, 26 Jun 2020 10:11:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:11:11: #2 number of paired peaks: 119 WARNING @ Fri, 26 Jun 2020 10:11:11: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Fri, 26 Jun 2020 10:11:11: start model_add_line... INFO @ Fri, 26 Jun 2020 10:11:12: start X-correlation... INFO @ Fri, 26 Jun 2020 10:11:12: end of X-cor INFO @ Fri, 26 Jun 2020 10:11:12: #2 finished! INFO @ Fri, 26 Jun 2020 10:11:12: #2 predicted fragment length is 67 bps INFO @ Fri, 26 Jun 2020 10:11:12: #2 alternative fragment length(s) may be 67,133,541,583,597 bps INFO @ Fri, 26 Jun 2020 10:11:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.20_model.r INFO @ Fri, 26 Jun 2020 10:11:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:11:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.10_summits.bed INFO @ Fri, 26 Jun 2020 10:11:15: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1446 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:11:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:11:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:11:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:11:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX974394/SRX974394.20_summits.bed INFO @ Fri, 26 Jun 2020 10:11:54: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling