Job ID = 6498744 SRX = SRX749080 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:56:15 prefetch.2.10.7: 1) Downloading 'SRR1636808'... 2020-06-25T23:56:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:59:40 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:59:40 prefetch.2.10.7: 1) 'SRR1636808' was downloaded successfully Read 20230113 spots for SRR1636808/SRR1636808.sra Written 20230113 spots for SRR1636808/SRR1636808.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: 00:38:10 20230113 reads; of these: 20230113 (100.00%) were paired; of these: 1171901 (5.79%) aligned concordantly 0 times 14144851 (69.92%) aligned concordantly exactly 1 time 4913361 (24.29%) aligned concordantly >1 times ---- 1171901 pairs aligned concordantly 0 times; of these: 11594 (0.99%) aligned discordantly 1 time ---- 1160307 pairs aligned 0 times concordantly or discordantly; of these: 2320614 mates make up the pairs; of these: 1809320 (77.97%) aligned 0 times 374975 (16.16%) aligned exactly 1 time 136319 (5.87%) aligned >1 times 95.53% overall alignment rate Time searching: 00:38:10 Overall time: 00:38:10 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] 2384889 / 19051863 = 0.1252 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 09:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.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 09:49:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:49:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:50:00: 1000000 INFO @ Fri, 26 Jun 2020 09:50:06: 2000000 INFO @ Fri, 26 Jun 2020 09:50:11: 3000000 INFO @ Fri, 26 Jun 2020 09:50:16: 4000000 INFO @ Fri, 26 Jun 2020 09:50:22: 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 09:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.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 09:50:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:50:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:50:27: 6000000 INFO @ Fri, 26 Jun 2020 09:50:34: 1000000 INFO @ Fri, 26 Jun 2020 09:50:34: 7000000 INFO @ Fri, 26 Jun 2020 09:50:41: 8000000 INFO @ Fri, 26 Jun 2020 09:50:41: 2000000 INFO @ Fri, 26 Jun 2020 09:50:47: 9000000 INFO @ Fri, 26 Jun 2020 09:50:48: 3000000 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 09:50:54: 10000000 INFO @ Fri, 26 Jun 2020 09:50:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.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 09:50:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:50:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:50:55: 4000000 INFO @ Fri, 26 Jun 2020 09:51:01: 11000000 INFO @ Fri, 26 Jun 2020 09:51:02: 1000000 INFO @ Fri, 26 Jun 2020 09:51:03: 5000000 INFO @ Fri, 26 Jun 2020 09:51:07: 12000000 INFO @ Fri, 26 Jun 2020 09:51:09: 2000000 INFO @ Fri, 26 Jun 2020 09:51:10: 6000000 INFO @ Fri, 26 Jun 2020 09:51:14: 13000000 INFO @ Fri, 26 Jun 2020 09:51:15: 3000000 INFO @ Fri, 26 Jun 2020 09:51:17: 7000000 INFO @ Fri, 26 Jun 2020 09:51:21: 14000000 INFO @ Fri, 26 Jun 2020 09:51:22: 4000000 INFO @ Fri, 26 Jun 2020 09:51:25: 8000000 INFO @ Fri, 26 Jun 2020 09:51:27: 15000000 INFO @ Fri, 26 Jun 2020 09:51:29: 5000000 INFO @ Fri, 26 Jun 2020 09:51:32: 9000000 INFO @ Fri, 26 Jun 2020 09:51:34: 16000000 INFO @ Fri, 26 Jun 2020 09:51:35: 6000000 INFO @ Fri, 26 Jun 2020 09:51:39: 10000000 INFO @ Fri, 26 Jun 2020 09:51:41: 17000000 INFO @ Fri, 26 Jun 2020 09:51:42: 7000000 INFO @ Fri, 26 Jun 2020 09:51:46: 11000000 INFO @ Fri, 26 Jun 2020 09:51:47: 18000000 INFO @ Fri, 26 Jun 2020 09:51:49: 8000000 INFO @ Fri, 26 Jun 2020 09:51:54: 12000000 INFO @ Fri, 26 Jun 2020 09:51:54: 19000000 INFO @ Fri, 26 Jun 2020 09:51:55: 9000000 INFO @ Fri, 26 Jun 2020 09:52:01: 20000000 INFO @ Fri, 26 Jun 2020 09:52:01: 13000000 INFO @ Fri, 26 Jun 2020 09:52:02: 10000000 INFO @ Fri, 26 Jun 2020 09:52:07: 21000000 INFO @ Fri, 26 Jun 2020 09:52:08: 14000000 INFO @ Fri, 26 Jun 2020 09:52:09: 11000000 INFO @ Fri, 26 Jun 2020 09:52:14: 22000000 INFO @ Fri, 26 Jun 2020 09:52:15: 12000000 INFO @ Fri, 26 Jun 2020 09:52:16: 15000000 INFO @ Fri, 26 Jun 2020 09:52:20: 23000000 INFO @ Fri, 26 Jun 2020 09:52:22: 13000000 INFO @ Fri, 26 Jun 2020 09:52:23: 16000000 INFO @ Fri, 26 Jun 2020 09:52:27: 24000000 INFO @ Fri, 26 Jun 2020 09:52:28: 14000000 INFO @ Fri, 26 Jun 2020 09:52:30: 17000000 INFO @ Fri, 26 Jun 2020 09:52:34: 25000000 INFO @ Fri, 26 Jun 2020 09:52:35: 15000000 INFO @ Fri, 26 Jun 2020 09:52:37: 18000000 INFO @ Fri, 26 Jun 2020 09:52:40: 26000000 INFO @ Fri, 26 Jun 2020 09:52:41: 16000000 INFO @ Fri, 26 Jun 2020 09:52:44: 19000000 INFO @ Fri, 26 Jun 2020 09:52:47: 27000000 INFO @ Fri, 26 Jun 2020 09:52:48: 17000000 INFO @ Fri, 26 Jun 2020 09:52:52: 20000000 INFO @ Fri, 26 Jun 2020 09:52:53: 28000000 INFO @ Fri, 26 Jun 2020 09:52:54: 18000000 INFO @ Fri, 26 Jun 2020 09:52:59: 21000000 INFO @ Fri, 26 Jun 2020 09:53:00: 29000000 INFO @ Fri, 26 Jun 2020 09:53:01: 19000000 INFO @ Fri, 26 Jun 2020 09:53:06: 22000000 INFO @ Fri, 26 Jun 2020 09:53:07: 30000000 INFO @ Fri, 26 Jun 2020 09:53:07: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:53:13: 23000000 INFO @ Fri, 26 Jun 2020 09:53:13: 31000000 INFO @ Fri, 26 Jun 2020 09:53:13: 21000000 INFO @ Fri, 26 Jun 2020 09:53:20: 32000000 INFO @ Fri, 26 Jun 2020 09:53:20: 24000000 INFO @ Fri, 26 Jun 2020 09:53:20: 22000000 INFO @ Fri, 26 Jun 2020 09:53:26: 33000000 INFO @ Fri, 26 Jun 2020 09:53:26: 23000000 INFO @ Fri, 26 Jun 2020 09:53:27: 25000000 INFO @ Fri, 26 Jun 2020 09:53:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:53:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:53:32: #1 total tags in treatment: 16674007 INFO @ Fri, 26 Jun 2020 09:53:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:53:32: #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 09:53:32: #1 tags after filtering in treatment: 14652597 INFO @ Fri, 26 Jun 2020 09:53:32: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:53:32: #1 finished! INFO @ Fri, 26 Jun 2020 09:53:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:53:33: 24000000 INFO @ Fri, 26 Jun 2020 09:53:33: #2 number of paired peaks: 962 WARNING @ Fri, 26 Jun 2020 09:53:33: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Fri, 26 Jun 2020 09:53:33: start model_add_line... INFO @ Fri, 26 Jun 2020 09:53:33: start X-correlation... INFO @ Fri, 26 Jun 2020 09:53:33: end of X-cor INFO @ Fri, 26 Jun 2020 09:53:33: #2 finished! INFO @ Fri, 26 Jun 2020 09:53:33: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 09:53:33: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 09:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.05_model.r INFO @ Fri, 26 Jun 2020 09:53:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:53:34: 26000000 INFO @ Fri, 26 Jun 2020 09:53:39: 25000000 INFO @ Fri, 26 Jun 2020 09:53:41: 27000000 INFO @ Fri, 26 Jun 2020 09:53:46: 26000000 INFO @ Fri, 26 Jun 2020 09:53:48: 28000000 INFO @ Fri, 26 Jun 2020 09:53:52: 27000000 INFO @ Fri, 26 Jun 2020 09:53:55: 29000000 INFO @ Fri, 26 Jun 2020 09:53:58: 28000000 INFO @ Fri, 26 Jun 2020 09:54:01: 30000000 INFO @ Fri, 26 Jun 2020 09:54:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:54:05: 29000000 INFO @ Fri, 26 Jun 2020 09:54:08: 31000000 INFO @ Fri, 26 Jun 2020 09:54:11: 30000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:54:15: 32000000 INFO @ Fri, 26 Jun 2020 09:54:17: 31000000 INFO @ Fri, 26 Jun 2020 09:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.05_summits.bed INFO @ Fri, 26 Jun 2020 09:54:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8342 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:54:22: 33000000 INFO @ Fri, 26 Jun 2020 09:54:24: 32000000 INFO @ Fri, 26 Jun 2020 09:54:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:54:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:54:28: #1 total tags in treatment: 16674007 INFO @ Fri, 26 Jun 2020 09:54:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:54:28: #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 09:54:28: #1 tags after filtering in treatment: 14652597 INFO @ Fri, 26 Jun 2020 09:54:28: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:54:28: #1 finished! INFO @ Fri, 26 Jun 2020 09:54:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:54:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:54:29: #2 number of paired peaks: 962 WARNING @ Fri, 26 Jun 2020 09:54:29: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Fri, 26 Jun 2020 09:54:29: start model_add_line... INFO @ Fri, 26 Jun 2020 09:54:29: start X-correlation... INFO @ Fri, 26 Jun 2020 09:54:29: end of X-cor INFO @ Fri, 26 Jun 2020 09:54:29: #2 finished! INFO @ Fri, 26 Jun 2020 09:54:29: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 09:54:29: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 09:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.10_model.r INFO @ Fri, 26 Jun 2020 09:54:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:54:30: 33000000 INFO @ Fri, 26 Jun 2020 09:54:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:54:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:54:35: #1 total tags in treatment: 16674007 INFO @ Fri, 26 Jun 2020 09:54:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:54:35: #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 09:54:35: #1 tags after filtering in treatment: 14652597 INFO @ Fri, 26 Jun 2020 09:54:35: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:54:35: #1 finished! INFO @ Fri, 26 Jun 2020 09:54:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:54:36: #2 number of paired peaks: 962 WARNING @ Fri, 26 Jun 2020 09:54:36: Fewer paired peaks (962) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 962 pairs to build model! INFO @ Fri, 26 Jun 2020 09:54:36: start model_add_line... INFO @ Fri, 26 Jun 2020 09:54:36: start X-correlation... INFO @ Fri, 26 Jun 2020 09:54:36: end of X-cor INFO @ Fri, 26 Jun 2020 09:54:36: #2 finished! INFO @ Fri, 26 Jun 2020 09:54:36: #2 predicted fragment length is 147 bps INFO @ Fri, 26 Jun 2020 09:54:36: #2 alternative fragment length(s) may be 147 bps INFO @ Fri, 26 Jun 2020 09:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.20_model.r INFO @ Fri, 26 Jun 2020 09:54:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:54:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:55:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:55:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:55:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:55:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.10_summits.bed INFO @ Fri, 26 Jun 2020 09:55:15: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6131 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:55:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749080/SRX749080.20_summits.bed INFO @ Fri, 26 Jun 2020 09:55:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4404 records, 4 fields): 5 millis CompletedMACS2peakCalling