Job ID = 14168199 SRX = ERX3978951 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 43313373 spots for ERR3976022/ERR3976022.sra Written 43313373 spots for ERR3976022/ERR3976022.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169454 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:36:06 43313373 reads; of these: 43313373 (100.00%) were paired; of these: 5888930 (13.60%) aligned concordantly 0 times 28942190 (66.82%) aligned concordantly exactly 1 time 8482253 (19.58%) aligned concordantly >1 times ---- 5888930 pairs aligned concordantly 0 times; of these: 1022056 (17.36%) aligned discordantly 1 time ---- 4866874 pairs aligned 0 times concordantly or discordantly; of these: 9733748 mates make up the pairs; of these: 6306469 (64.79%) aligned 0 times 1610443 (16.54%) aligned exactly 1 time 1816836 (18.67%) aligned >1 times 92.72% overall alignment rate Time searching: 01:36:07 Overall time: 01:36:07 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 36 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] 23917207 / 38262221 = 0.6251 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.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, 10 Dec 2021 18:05:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:05:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:05:57: 1000000 INFO @ Fri, 10 Dec 2021 18:06:02: 2000000 INFO @ Fri, 10 Dec 2021 18:06:08: 3000000 INFO @ Fri, 10 Dec 2021 18:06:13: 4000000 INFO @ Fri, 10 Dec 2021 18:06:18: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:06:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.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, 10 Dec 2021 18:06:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:06:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:06:24: 6000000 INFO @ Fri, 10 Dec 2021 18:06:27: 1000000 INFO @ Fri, 10 Dec 2021 18:06:30: 7000000 INFO @ Fri, 10 Dec 2021 18:06:34: 2000000 INFO @ Fri, 10 Dec 2021 18:06:37: 8000000 INFO @ Fri, 10 Dec 2021 18:06:40: 3000000 INFO @ Fri, 10 Dec 2021 18:06:43: 9000000 INFO @ Fri, 10 Dec 2021 18:06:46: 4000000 INFO @ Fri, 10 Dec 2021 18:06:49: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 18:06:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.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, 10 Dec 2021 18:06:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:06:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:06:52: 5000000 INFO @ Fri, 10 Dec 2021 18:06:55: 11000000 INFO @ Fri, 10 Dec 2021 18:06:57: 1000000 INFO @ Fri, 10 Dec 2021 18:06:59: 6000000 INFO @ Fri, 10 Dec 2021 18:07:01: 12000000 INFO @ Fri, 10 Dec 2021 18:07:04: 2000000 INFO @ Fri, 10 Dec 2021 18:07:05: 7000000 INFO @ Fri, 10 Dec 2021 18:07:08: 13000000 INFO @ Fri, 10 Dec 2021 18:07:10: 3000000 INFO @ Fri, 10 Dec 2021 18:07:11: 8000000 INFO @ Fri, 10 Dec 2021 18:07:14: 14000000 INFO @ Fri, 10 Dec 2021 18:07:16: 4000000 INFO @ Fri, 10 Dec 2021 18:07:17: 9000000 INFO @ Fri, 10 Dec 2021 18:07:20: 15000000 INFO @ Fri, 10 Dec 2021 18:07:22: 5000000 INFO @ Fri, 10 Dec 2021 18:07:24: 10000000 INFO @ Fri, 10 Dec 2021 18:07:26: 16000000 INFO @ Fri, 10 Dec 2021 18:07:29: 6000000 INFO @ Fri, 10 Dec 2021 18:07:30: 11000000 INFO @ Fri, 10 Dec 2021 18:07:33: 17000000 INFO @ Fri, 10 Dec 2021 18:07:35: 7000000 INFO @ Fri, 10 Dec 2021 18:07:36: 12000000 INFO @ Fri, 10 Dec 2021 18:07:39: 18000000 INFO @ Fri, 10 Dec 2021 18:07:41: 8000000 INFO @ Fri, 10 Dec 2021 18:07:42: 13000000 INFO @ Fri, 10 Dec 2021 18:07:45: 19000000 INFO @ Fri, 10 Dec 2021 18:07:47: 9000000 INFO @ Fri, 10 Dec 2021 18:07:49: 14000000 INFO @ Fri, 10 Dec 2021 18:07:51: 20000000 INFO @ Fri, 10 Dec 2021 18:07:54: 10000000 INFO @ Fri, 10 Dec 2021 18:07:55: 15000000 INFO @ Fri, 10 Dec 2021 18:07:57: 21000000 INFO @ Fri, 10 Dec 2021 18:08:00: 11000000 INFO @ Fri, 10 Dec 2021 18:08:01: 16000000 INFO @ Fri, 10 Dec 2021 18:08:04: 22000000 INFO @ Fri, 10 Dec 2021 18:08:06: 12000000 INFO @ Fri, 10 Dec 2021 18:08:07: 17000000 INFO @ Fri, 10 Dec 2021 18:08:10: 23000000 INFO @ Fri, 10 Dec 2021 18:08:12: 13000000 INFO @ Fri, 10 Dec 2021 18:08:14: 18000000 INFO @ Fri, 10 Dec 2021 18:08:16: 24000000 INFO @ Fri, 10 Dec 2021 18:08:18: 14000000 INFO @ Fri, 10 Dec 2021 18:08:20: 19000000 INFO @ Fri, 10 Dec 2021 18:08:23: 25000000 INFO @ Fri, 10 Dec 2021 18:08:25: 15000000 INFO @ Fri, 10 Dec 2021 18:08:26: 20000000 INFO @ Fri, 10 Dec 2021 18:08:29: 26000000 INFO @ Fri, 10 Dec 2021 18:08:31: 16000000 INFO @ Fri, 10 Dec 2021 18:08:32: 21000000 INFO @ Fri, 10 Dec 2021 18:08:35: 27000000 INFO @ Fri, 10 Dec 2021 18:08:37: 17000000 INFO @ Fri, 10 Dec 2021 18:08:39: 22000000 INFO @ Fri, 10 Dec 2021 18:08:42: 28000000 INFO @ Fri, 10 Dec 2021 18:08:43: 18000000 INFO @ Fri, 10 Dec 2021 18:08:45: 23000000 INFO @ Fri, 10 Dec 2021 18:08:48: 29000000 INFO @ Fri, 10 Dec 2021 18:08:50: 19000000 INFO @ Fri, 10 Dec 2021 18:08:51: 24000000 INFO @ Fri, 10 Dec 2021 18:08:54: 30000000 INFO @ Fri, 10 Dec 2021 18:08:56: 20000000 INFO @ Fri, 10 Dec 2021 18:08:58: 25000000 INFO @ Fri, 10 Dec 2021 18:09:01: 31000000 INFO @ Fri, 10 Dec 2021 18:09:02: 21000000 INFO @ Fri, 10 Dec 2021 18:09:04: 26000000 INFO @ Fri, 10 Dec 2021 18:09:07: 32000000 INFO @ Fri, 10 Dec 2021 18:09:08: 22000000 INFO @ Fri, 10 Dec 2021 18:09:10: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:09:10: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:09:10: #1 total tags in treatment: 14163039 INFO @ Fri, 10 Dec 2021 18:09:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:09:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:09:11: 27000000 INFO @ Fri, 10 Dec 2021 18:09:11: #1 tags after filtering in treatment: 12920367 INFO @ Fri, 10 Dec 2021 18:09:11: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 18:09:11: #1 finished! INFO @ Fri, 10 Dec 2021 18:09:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:09:11: #2 number of paired peaks: 616 WARNING @ Fri, 10 Dec 2021 18:09:11: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Fri, 10 Dec 2021 18:09:11: start model_add_line... INFO @ Fri, 10 Dec 2021 18:09:12: start X-correlation... INFO @ Fri, 10 Dec 2021 18:09:12: end of X-cor INFO @ Fri, 10 Dec 2021 18:09:12: #2 finished! INFO @ Fri, 10 Dec 2021 18:09:12: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 18:09:12: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 18:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.05_model.r INFO @ Fri, 10 Dec 2021 18:09:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:09:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:09:15: 23000000 INFO @ Fri, 10 Dec 2021 18:09:17: 28000000 INFO @ Fri, 10 Dec 2021 18:09:21: 24000000 INFO @ Fri, 10 Dec 2021 18:09:23: 29000000 INFO @ Fri, 10 Dec 2021 18:09:27: 25000000 INFO @ Fri, 10 Dec 2021 18:09:29: 30000000 INFO @ Fri, 10 Dec 2021 18:09:33: 26000000 INFO @ Fri, 10 Dec 2021 18:09:35: 31000000 INFO @ Fri, 10 Dec 2021 18:09:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:09:39: 27000000 INFO @ Fri, 10 Dec 2021 18:09:42: 32000000 INFO @ Fri, 10 Dec 2021 18:09:45: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:09:45: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:09:45: #1 total tags in treatment: 14163039 INFO @ Fri, 10 Dec 2021 18:09:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:09:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:09:45: #1 tags after filtering in treatment: 12920367 INFO @ Fri, 10 Dec 2021 18:09:45: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 18:09:45: #1 finished! INFO @ Fri, 10 Dec 2021 18:09:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:09:45: 28000000 INFO @ Fri, 10 Dec 2021 18:09:46: #2 number of paired peaks: 616 WARNING @ Fri, 10 Dec 2021 18:09:46: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Fri, 10 Dec 2021 18:09:46: start model_add_line... INFO @ Fri, 10 Dec 2021 18:09:46: start X-correlation... INFO @ Fri, 10 Dec 2021 18:09:46: end of X-cor INFO @ Fri, 10 Dec 2021 18:09:46: #2 finished! INFO @ Fri, 10 Dec 2021 18:09:46: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 18:09:46: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 18:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.10_model.r INFO @ Fri, 10 Dec 2021 18:09:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.05_summits.bed INFO @ Fri, 10 Dec 2021 18:09:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10465 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:09:51: 29000000 INFO @ Fri, 10 Dec 2021 18:09:57: 30000000 INFO @ Fri, 10 Dec 2021 18:10:03: 31000000 INFO @ Fri, 10 Dec 2021 18:10:09: 32000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:10:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:12: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:10:12: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:10:12: #1 total tags in treatment: 14163039 INFO @ Fri, 10 Dec 2021 18:10:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:10:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:10:12: #1 tags after filtering in treatment: 12920367 INFO @ Fri, 10 Dec 2021 18:10:12: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 18:10:12: #1 finished! INFO @ Fri, 10 Dec 2021 18:10:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:10:13: #2 number of paired peaks: 616 WARNING @ Fri, 10 Dec 2021 18:10:13: Fewer paired peaks (616) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 616 pairs to build model! INFO @ Fri, 10 Dec 2021 18:10:13: start model_add_line... INFO @ Fri, 10 Dec 2021 18:10:13: start X-correlation... INFO @ Fri, 10 Dec 2021 18:10:13: end of X-cor INFO @ Fri, 10 Dec 2021 18:10:13: #2 finished! INFO @ Fri, 10 Dec 2021 18:10:13: #2 predicted fragment length is 162 bps INFO @ Fri, 10 Dec 2021 18:10:13: #2 alternative fragment length(s) may be 162 bps INFO @ Fri, 10 Dec 2021 18:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.20_model.r INFO @ Fri, 10 Dec 2021 18:10:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:10:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.10_summits.bed INFO @ Fri, 10 Dec 2021 18:10:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5648 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:10:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978951/ERX3978951.20_summits.bed INFO @ Fri, 10 Dec 2021 18:10:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2381 records, 4 fields): 4 millis CompletedMACS2peakCalling