Job ID = 14171760 SRX = SRX10386231 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22548065 spots for SRR14009296/SRR14009296.sra Written 22548065 spots for SRR14009296/SRR14009296.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172342 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:38:30 22548065 reads; of these: 22548065 (100.00%) were paired; of these: 8900742 (39.47%) aligned concordantly 0 times 8911786 (39.52%) aligned concordantly exactly 1 time 4735537 (21.00%) aligned concordantly >1 times ---- 8900742 pairs aligned concordantly 0 times; of these: 464509 (5.22%) aligned discordantly 1 time ---- 8436233 pairs aligned 0 times concordantly or discordantly; of these: 16872466 mates make up the pairs; of these: 12563932 (74.46%) aligned 0 times 2783365 (16.50%) aligned exactly 1 time 1525169 (9.04%) aligned >1 times 72.14% overall alignment rate Time searching: 00:38:30 Overall time: 00:38:30 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] 1247000 / 13769827 = 0.0906 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 @ Sat, 11 Dec 2021 13:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.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 @ Sat, 11 Dec 2021 13:31:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:31:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:31:18: 1000000 INFO @ Sat, 11 Dec 2021 13:31:24: 2000000 INFO @ Sat, 11 Dec 2021 13:31:30: 3000000 INFO @ Sat, 11 Dec 2021 13:31:36: 4000000 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 @ Sat, 11 Dec 2021 13:31:41: 5000000 INFO @ Sat, 11 Dec 2021 13:31:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.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 @ Sat, 11 Dec 2021 13:31:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:31:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:31:48: 6000000 INFO @ Sat, 11 Dec 2021 13:31:48: 1000000 INFO @ Sat, 11 Dec 2021 13:31:54: 2000000 INFO @ Sat, 11 Dec 2021 13:31:54: 7000000 INFO @ Sat, 11 Dec 2021 13:31:59: 3000000 INFO @ Sat, 11 Dec 2021 13:32:01: 8000000 INFO @ Sat, 11 Dec 2021 13:32:05: 4000000 INFO @ Sat, 11 Dec 2021 13:32:07: 9000000 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 @ Sat, 11 Dec 2021 13:32:11: 5000000 INFO @ Sat, 11 Dec 2021 13:32:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.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 @ Sat, 11 Dec 2021 13:32:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:13: 10000000 INFO @ Sat, 11 Dec 2021 13:32:16: 6000000 INFO @ Sat, 11 Dec 2021 13:32:18: 1000000 INFO @ Sat, 11 Dec 2021 13:32:20: 11000000 INFO @ Sat, 11 Dec 2021 13:32:22: 7000000 INFO @ Sat, 11 Dec 2021 13:32:25: 2000000 INFO @ Sat, 11 Dec 2021 13:32:26: 12000000 INFO @ Sat, 11 Dec 2021 13:32:28: 8000000 INFO @ Sat, 11 Dec 2021 13:32:31: 3000000 INFO @ Sat, 11 Dec 2021 13:32:33: 13000000 INFO @ Sat, 11 Dec 2021 13:32:34: 9000000 INFO @ Sat, 11 Dec 2021 13:32:37: 4000000 INFO @ Sat, 11 Dec 2021 13:32:39: 14000000 INFO @ Sat, 11 Dec 2021 13:32:40: 10000000 INFO @ Sat, 11 Dec 2021 13:32:44: 5000000 INFO @ Sat, 11 Dec 2021 13:32:45: 11000000 INFO @ Sat, 11 Dec 2021 13:32:46: 15000000 INFO @ Sat, 11 Dec 2021 13:32:50: 6000000 INFO @ Sat, 11 Dec 2021 13:32:51: 12000000 INFO @ Sat, 11 Dec 2021 13:32:52: 16000000 INFO @ Sat, 11 Dec 2021 13:32:56: 7000000 INFO @ Sat, 11 Dec 2021 13:32:57: 13000000 INFO @ Sat, 11 Dec 2021 13:32:59: 17000000 INFO @ Sat, 11 Dec 2021 13:33:02: 8000000 INFO @ Sat, 11 Dec 2021 13:33:03: 14000000 INFO @ Sat, 11 Dec 2021 13:33:05: 18000000 INFO @ Sat, 11 Dec 2021 13:33:09: 9000000 INFO @ Sat, 11 Dec 2021 13:33:09: 15000000 INFO @ Sat, 11 Dec 2021 13:33:12: 19000000 INFO @ Sat, 11 Dec 2021 13:33:15: 16000000 INFO @ Sat, 11 Dec 2021 13:33:15: 10000000 INFO @ Sat, 11 Dec 2021 13:33:18: 20000000 INFO @ Sat, 11 Dec 2021 13:33:20: 17000000 INFO @ Sat, 11 Dec 2021 13:33:21: 11000000 INFO @ Sat, 11 Dec 2021 13:33:24: 21000000 INFO @ Sat, 11 Dec 2021 13:33:26: 18000000 INFO @ Sat, 11 Dec 2021 13:33:27: 12000000 INFO @ Sat, 11 Dec 2021 13:33:30: 22000000 INFO @ Sat, 11 Dec 2021 13:33:32: 19000000 INFO @ Sat, 11 Dec 2021 13:33:34: 13000000 INFO @ Sat, 11 Dec 2021 13:33:37: 23000000 INFO @ Sat, 11 Dec 2021 13:33:38: 20000000 INFO @ Sat, 11 Dec 2021 13:33:40: 14000000 INFO @ Sat, 11 Dec 2021 13:33:44: 21000000 INFO @ Sat, 11 Dec 2021 13:33:44: 24000000 INFO @ Sat, 11 Dec 2021 13:33:46: 15000000 INFO @ Sat, 11 Dec 2021 13:33:49: 22000000 INFO @ Sat, 11 Dec 2021 13:33:50: 25000000 INFO @ Sat, 11 Dec 2021 13:33:53: 16000000 INFO @ Sat, 11 Dec 2021 13:33:55: 23000000 INFO @ Sat, 11 Dec 2021 13:33:57: 26000000 INFO @ Sat, 11 Dec 2021 13:33:59: 17000000 INFO @ Sat, 11 Dec 2021 13:34:01: 24000000 INFO @ Sat, 11 Dec 2021 13:34:04: 27000000 INFO @ Sat, 11 Dec 2021 13:34:05: 18000000 INFO @ Sat, 11 Dec 2021 13:34:07: 25000000 INFO @ Sat, 11 Dec 2021 13:34:10: 28000000 INFO @ Sat, 11 Dec 2021 13:34:11: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:34:12: 26000000 INFO @ Sat, 11 Dec 2021 13:34:17: 29000000 INFO @ Sat, 11 Dec 2021 13:34:18: 20000000 INFO @ Sat, 11 Dec 2021 13:34:18: 27000000 INFO @ Sat, 11 Dec 2021 13:34:23: 30000000 INFO @ Sat, 11 Dec 2021 13:34:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:34:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:34:24: #1 total tags in treatment: 12401063 INFO @ Sat, 11 Dec 2021 13:34:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:34:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:34:24: #1 tags after filtering in treatment: 10912620 INFO @ Sat, 11 Dec 2021 13:34:24: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:34:24: #1 finished! INFO @ Sat, 11 Dec 2021 13:34:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:34:24: 21000000 INFO @ Sat, 11 Dec 2021 13:34:24: 28000000 INFO @ Sat, 11 Dec 2021 13:34:25: #2 number of paired peaks: 173 WARNING @ Sat, 11 Dec 2021 13:34:25: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 11 Dec 2021 13:34:25: start model_add_line... INFO @ Sat, 11 Dec 2021 13:34:25: start X-correlation... INFO @ Sat, 11 Dec 2021 13:34:25: end of X-cor INFO @ Sat, 11 Dec 2021 13:34:25: #2 finished! INFO @ Sat, 11 Dec 2021 13:34:25: #2 predicted fragment length is 116 bps INFO @ Sat, 11 Dec 2021 13:34:25: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 11 Dec 2021 13:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.05_model.r INFO @ Sat, 11 Dec 2021 13:34:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:34:30: 29000000 INFO @ Sat, 11 Dec 2021 13:34:30: 22000000 INFO @ Sat, 11 Dec 2021 13:34:35: 30000000 INFO @ Sat, 11 Dec 2021 13:34:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:34:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:34:36: #1 total tags in treatment: 12401063 INFO @ Sat, 11 Dec 2021 13:34:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:34:36: #1 tags after filtering in treatment: 10912620 INFO @ Sat, 11 Dec 2021 13:34:36: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:34:36: #1 finished! INFO @ Sat, 11 Dec 2021 13:34:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:34:36: 23000000 INFO @ Sat, 11 Dec 2021 13:34:37: #2 number of paired peaks: 173 WARNING @ Sat, 11 Dec 2021 13:34:37: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 11 Dec 2021 13:34:37: start model_add_line... INFO @ Sat, 11 Dec 2021 13:34:37: start X-correlation... INFO @ Sat, 11 Dec 2021 13:34:37: end of X-cor INFO @ Sat, 11 Dec 2021 13:34:37: #2 finished! INFO @ Sat, 11 Dec 2021 13:34:37: #2 predicted fragment length is 116 bps INFO @ Sat, 11 Dec 2021 13:34:37: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 11 Dec 2021 13:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.10_model.r INFO @ Sat, 11 Dec 2021 13:34:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:34:42: 24000000 INFO @ Sat, 11 Dec 2021 13:34:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:34:48: 25000000 INFO @ Sat, 11 Dec 2021 13:34:54: 26000000 INFO @ Sat, 11 Dec 2021 13:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.05_summits.bed INFO @ Sat, 11 Dec 2021 13:34:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1300 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:34:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:35:00: 27000000 INFO @ Sat, 11 Dec 2021 13:35:06: 28000000 INFO @ Sat, 11 Dec 2021 13:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.10_summits.bed INFO @ Sat, 11 Dec 2021 13:35:09: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (857 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:35:12: 29000000 INFO @ Sat, 11 Dec 2021 13:35:18: 30000000 INFO @ Sat, 11 Dec 2021 13:35:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:35:18: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:35:18: #1 total tags in treatment: 12401063 INFO @ Sat, 11 Dec 2021 13:35:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:35:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:35:18: #1 tags after filtering in treatment: 10912620 INFO @ Sat, 11 Dec 2021 13:35:18: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:35:18: #1 finished! INFO @ Sat, 11 Dec 2021 13:35:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:35:19: #2 number of paired peaks: 173 WARNING @ Sat, 11 Dec 2021 13:35:19: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 11 Dec 2021 13:35:19: start model_add_line... INFO @ Sat, 11 Dec 2021 13:35:19: start X-correlation... INFO @ Sat, 11 Dec 2021 13:35:19: end of X-cor INFO @ Sat, 11 Dec 2021 13:35:19: #2 finished! INFO @ Sat, 11 Dec 2021 13:35:19: #2 predicted fragment length is 116 bps INFO @ Sat, 11 Dec 2021 13:35:19: #2 alternative fragment length(s) may be 116 bps INFO @ Sat, 11 Dec 2021 13:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.20_model.r INFO @ Sat, 11 Dec 2021 13:35:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:35:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386231/SRX10386231.20_summits.bed INFO @ Sat, 11 Dec 2021 13:35:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (543 records, 4 fields): 1 millis CompletedMACS2peakCalling