Job ID = 14168207 SRX = ERX3978954 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 54205224 spots for ERR3976025/ERR3976025.sra Written 54205224 spots for ERR3976025/ERR3976025.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169644 ("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: 02:43:51 54205224 reads; of these: 54205224 (100.00%) were paired; of these: 7444292 (13.73%) aligned concordantly 0 times 35546496 (65.58%) aligned concordantly exactly 1 time 11214436 (20.69%) aligned concordantly >1 times ---- 7444292 pairs aligned concordantly 0 times; of these: 1086096 (14.59%) aligned discordantly 1 time ---- 6358196 pairs aligned 0 times concordantly or discordantly; of these: 12716392 mates make up the pairs; of these: 6186029 (48.65%) aligned 0 times 3041720 (23.92%) aligned exactly 1 time 3488643 (27.43%) aligned >1 times 94.29% overall alignment rate Time searching: 02:43:51 Overall time: 02:43:51 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 44 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] 34953574 / 47587731 = 0.7345 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 19:17:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.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 19:17:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:17:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:17:38: 1000000 INFO @ Fri, 10 Dec 2021 19:17:45: 2000000 INFO @ Fri, 10 Dec 2021 19:17:52: 3000000 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 19:18:00: 4000000 INFO @ Fri, 10 Dec 2021 19:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.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 19:18:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:18:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:08: 5000000 INFO @ Fri, 10 Dec 2021 19:18:09: 1000000 INFO @ Fri, 10 Dec 2021 19:18:17: 6000000 INFO @ Fri, 10 Dec 2021 19:18:18: 2000000 INFO @ Fri, 10 Dec 2021 19:18:25: 7000000 INFO @ Fri, 10 Dec 2021 19:18:27: 3000000 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 19:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.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 19:18:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:18:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:34: 8000000 INFO @ Fri, 10 Dec 2021 19:18:35: 4000000 INFO @ Fri, 10 Dec 2021 19:18:38: 1000000 INFO @ Fri, 10 Dec 2021 19:18:42: 9000000 INFO @ Fri, 10 Dec 2021 19:18:44: 5000000 INFO @ Fri, 10 Dec 2021 19:18:46: 2000000 INFO @ Fri, 10 Dec 2021 19:18:51: 10000000 INFO @ Fri, 10 Dec 2021 19:18:53: 6000000 INFO @ Fri, 10 Dec 2021 19:18:54: 3000000 INFO @ Fri, 10 Dec 2021 19:18:59: 11000000 INFO @ Fri, 10 Dec 2021 19:19:02: 4000000 INFO @ Fri, 10 Dec 2021 19:19:02: 7000000 INFO @ Fri, 10 Dec 2021 19:19:08: 12000000 INFO @ Fri, 10 Dec 2021 19:19:10: 5000000 INFO @ Fri, 10 Dec 2021 19:19:11: 8000000 INFO @ Fri, 10 Dec 2021 19:19:16: 13000000 INFO @ Fri, 10 Dec 2021 19:19:18: 6000000 INFO @ Fri, 10 Dec 2021 19:19:20: 9000000 INFO @ Fri, 10 Dec 2021 19:19:25: 14000000 INFO @ Fri, 10 Dec 2021 19:19:26: 7000000 INFO @ Fri, 10 Dec 2021 19:19:29: 10000000 INFO @ Fri, 10 Dec 2021 19:19:34: 15000000 INFO @ Fri, 10 Dec 2021 19:19:34: 8000000 INFO @ Fri, 10 Dec 2021 19:19:38: 11000000 INFO @ Fri, 10 Dec 2021 19:19:42: 16000000 INFO @ Fri, 10 Dec 2021 19:19:42: 9000000 INFO @ Fri, 10 Dec 2021 19:19:47: 12000000 INFO @ Fri, 10 Dec 2021 19:19:51: 10000000 INFO @ Fri, 10 Dec 2021 19:19:51: 17000000 INFO @ Fri, 10 Dec 2021 19:19:55: 13000000 INFO @ Fri, 10 Dec 2021 19:19:59: 11000000 INFO @ Fri, 10 Dec 2021 19:19:59: 18000000 INFO @ Fri, 10 Dec 2021 19:20:04: 14000000 INFO @ Fri, 10 Dec 2021 19:20:07: 12000000 INFO @ Fri, 10 Dec 2021 19:20:08: 19000000 INFO @ Fri, 10 Dec 2021 19:20:12: 15000000 INFO @ Fri, 10 Dec 2021 19:20:15: 13000000 INFO @ Fri, 10 Dec 2021 19:20:17: 20000000 INFO @ Fri, 10 Dec 2021 19:20:21: 16000000 INFO @ Fri, 10 Dec 2021 19:20:23: 14000000 INFO @ Fri, 10 Dec 2021 19:20:26: 21000000 INFO @ Fri, 10 Dec 2021 19:20:29: 17000000 INFO @ Fri, 10 Dec 2021 19:20:31: 15000000 INFO @ Fri, 10 Dec 2021 19:20:34: 22000000 INFO @ Fri, 10 Dec 2021 19:20:38: 18000000 INFO @ Fri, 10 Dec 2021 19:20:39: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:20:43: 23000000 INFO @ Fri, 10 Dec 2021 19:20:47: 19000000 INFO @ Fri, 10 Dec 2021 19:20:47: 17000000 INFO @ Fri, 10 Dec 2021 19:20:52: 24000000 INFO @ Fri, 10 Dec 2021 19:20:55: 18000000 INFO @ Fri, 10 Dec 2021 19:20:55: 20000000 INFO @ Fri, 10 Dec 2021 19:21:01: 25000000 INFO @ Fri, 10 Dec 2021 19:21:03: 19000000 INFO @ Fri, 10 Dec 2021 19:21:04: 21000000 INFO @ Fri, 10 Dec 2021 19:21:10: 26000000 INFO @ Fri, 10 Dec 2021 19:21:11: 20000000 INFO @ Fri, 10 Dec 2021 19:21:13: 22000000 INFO @ Fri, 10 Dec 2021 19:21:19: 27000000 INFO @ Fri, 10 Dec 2021 19:21:20: 21000000 INFO @ Fri, 10 Dec 2021 19:21:22: 23000000 INFO @ Fri, 10 Dec 2021 19:21:28: 28000000 INFO @ Fri, 10 Dec 2021 19:21:28: 22000000 INFO @ Fri, 10 Dec 2021 19:21:30: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:21:36: 23000000 INFO @ Fri, 10 Dec 2021 19:21:36: 29000000 INFO @ Fri, 10 Dec 2021 19:21:39: 25000000 INFO @ Fri, 10 Dec 2021 19:21:44: 24000000 INFO @ Fri, 10 Dec 2021 19:21:46: 30000000 INFO @ Fri, 10 Dec 2021 19:21:48: 26000000 INFO @ Fri, 10 Dec 2021 19:21:52: 25000000 INFO @ Fri, 10 Dec 2021 19:21:54: 31000000 INFO @ Fri, 10 Dec 2021 19:21:56: 27000000 INFO @ Fri, 10 Dec 2021 19:22:01: 26000000 INFO @ Fri, 10 Dec 2021 19:22:03: 32000000 INFO @ Fri, 10 Dec 2021 19:22:05: 28000000 INFO @ Fri, 10 Dec 2021 19:22:06: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:22:06: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:22:06: #1 total tags in treatment: 12552741 INFO @ Fri, 10 Dec 2021 19:22:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:22:06: #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 19:22:06: #1 tags after filtering in treatment: 11132847 INFO @ Fri, 10 Dec 2021 19:22:06: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 19:22:06: #1 finished! INFO @ Fri, 10 Dec 2021 19:22:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:22:07: #2 number of paired peaks: 1368 INFO @ Fri, 10 Dec 2021 19:22:07: start model_add_line... INFO @ Fri, 10 Dec 2021 19:22:07: start X-correlation... INFO @ Fri, 10 Dec 2021 19:22:07: end of X-cor INFO @ Fri, 10 Dec 2021 19:22:07: #2 finished! INFO @ Fri, 10 Dec 2021 19:22:07: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 19:22:07: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 19:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.05_model.r INFO @ Fri, 10 Dec 2021 19:22:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:22:09: 27000000 INFO @ Fri, 10 Dec 2021 19:22:14: 29000000 INFO @ Fri, 10 Dec 2021 19:22:17: 28000000 INFO @ Fri, 10 Dec 2021 19:22:22: 30000000 INFO @ Fri, 10 Dec 2021 19:22:25: 29000000 INFO @ Fri, 10 Dec 2021 19:22:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:22:30: 31000000 INFO @ Fri, 10 Dec 2021 19:22:33: 30000000 INFO @ Fri, 10 Dec 2021 19:22:39: 32000000 INFO @ Fri, 10 Dec 2021 19:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.05_summits.bed INFO @ Fri, 10 Dec 2021 19:22:41: Done! INFO @ Fri, 10 Dec 2021 19:22:41: 31000000 INFO @ Fri, 10 Dec 2021 19:22:41: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:22:41: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:22:41: #1 total tags in treatment: 12552741 INFO @ Fri, 10 Dec 2021 19:22:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:22:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (14265 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:22:41: #1 tags after filtering in treatment: 11132847 INFO @ Fri, 10 Dec 2021 19:22:41: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 19:22:41: #1 finished! INFO @ Fri, 10 Dec 2021 19:22:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:22:42: #2 number of paired peaks: 1368 INFO @ Fri, 10 Dec 2021 19:22:42: start model_add_line... INFO @ Fri, 10 Dec 2021 19:22:42: start X-correlation... INFO @ Fri, 10 Dec 2021 19:22:42: end of X-cor INFO @ Fri, 10 Dec 2021 19:22:42: #2 finished! INFO @ Fri, 10 Dec 2021 19:22:42: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 19:22:42: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 19:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.10_model.r INFO @ Fri, 10 Dec 2021 19:22:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:22:48: 32000000 INFO @ Fri, 10 Dec 2021 19:22:51: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:22:51: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:22:51: #1 total tags in treatment: 12552741 INFO @ Fri, 10 Dec 2021 19:22:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:22:51: #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 19:22:51: #1 tags after filtering in treatment: 11132847 INFO @ Fri, 10 Dec 2021 19:22:51: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 19:22:51: #1 finished! INFO @ Fri, 10 Dec 2021 19:22:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:22:52: #2 number of paired peaks: 1368 INFO @ Fri, 10 Dec 2021 19:22:52: start model_add_line... INFO @ Fri, 10 Dec 2021 19:22:52: start X-correlation... INFO @ Fri, 10 Dec 2021 19:22:52: end of X-cor INFO @ Fri, 10 Dec 2021 19:22:52: #2 finished! INFO @ Fri, 10 Dec 2021 19:22:52: #2 predicted fragment length is 163 bps INFO @ Fri, 10 Dec 2021 19:22:52: #2 alternative fragment length(s) may be 163 bps INFO @ Fri, 10 Dec 2021 19:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.20_model.r INFO @ Fri, 10 Dec 2021 19:22:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.10_summits.bed INFO @ Fri, 10 Dec 2021 19:23:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9744 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978954/ERX3978954.20_summits.bed INFO @ Fri, 10 Dec 2021 19:23:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5317 records, 4 fields): 7 millis CompletedMACS2peakCalling