Job ID = 14168263 SRX = ERX3978841 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34660013 spots for ERR3975910/ERR3975910.sra Written 34660013 spots for ERR3975910/ERR3975910.sra Read 61609532 spots for ERR3975996/ERR3975996.sra Written 61609532 spots for ERR3975996/ERR3975996.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170107 ("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: 06:54:12 96269545 reads; of these: 96269545 (100.00%) were paired; of these: 31349690 (32.56%) aligned concordantly 0 times 52490424 (54.52%) aligned concordantly exactly 1 time 12429431 (12.91%) aligned concordantly >1 times ---- 31349690 pairs aligned concordantly 0 times; of these: 3979078 (12.69%) aligned discordantly 1 time ---- 27370612 pairs aligned 0 times concordantly or discordantly; of these: 54741224 mates make up the pairs; of these: 23433308 (42.81%) aligned 0 times 18730445 (34.22%) aligned exactly 1 time 12577471 (22.98%) aligned >1 times 87.83% overall alignment rate Time searching: 06:54:12 Overall time: 06:54:12 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 72 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] 63416751 / 68129906 = 0.9308 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 00:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.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 00:17:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:17:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:17:43: 1000000 INFO @ Sat, 11 Dec 2021 00:17:48: 2000000 INFO @ Sat, 11 Dec 2021 00:17:53: 3000000 INFO @ Sat, 11 Dec 2021 00:17:59: 4000000 INFO @ Sat, 11 Dec 2021 00:18:04: 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 @ Sat, 11 Dec 2021 00:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.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 00:18:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:18:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:18:09: 6000000 INFO @ Sat, 11 Dec 2021 00:18:12: 1000000 INFO @ Sat, 11 Dec 2021 00:18:15: 7000000 INFO @ Sat, 11 Dec 2021 00:18:17: 2000000 INFO @ Sat, 11 Dec 2021 00:18:20: 8000000 INFO @ Sat, 11 Dec 2021 00:18:23: 3000000 INFO @ Sat, 11 Dec 2021 00:18:25: 9000000 INFO @ Sat, 11 Dec 2021 00:18:28: 4000000 INFO @ Sat, 11 Dec 2021 00:18:31: 10000000 INFO @ Sat, 11 Dec 2021 00:18:34: 5000000 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 00:18:36: 11000000 INFO @ Sat, 11 Dec 2021 00:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.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 00:18:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:18:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:18:39: 6000000 INFO @ Sat, 11 Dec 2021 00:18:41: 12000000 INFO @ Sat, 11 Dec 2021 00:18:42: 1000000 INFO @ Sat, 11 Dec 2021 00:18:45: 7000000 INFO @ Sat, 11 Dec 2021 00:18:47: 13000000 INFO @ Sat, 11 Dec 2021 00:18:47: 2000000 INFO @ Sat, 11 Dec 2021 00:18:50: 8000000 INFO @ Sat, 11 Dec 2021 00:18:52: 14000000 INFO @ Sat, 11 Dec 2021 00:18:53: 3000000 INFO @ Sat, 11 Dec 2021 00:18:55: 9000000 INFO @ Sat, 11 Dec 2021 00:18:57: 15000000 INFO @ Sat, 11 Dec 2021 00:18:58: 4000000 INFO @ Sat, 11 Dec 2021 00:19:01: 10000000 INFO @ Sat, 11 Dec 2021 00:19:03: 16000000 INFO @ Sat, 11 Dec 2021 00:19:04: 5000000 INFO @ Sat, 11 Dec 2021 00:19:06: 11000000 INFO @ Sat, 11 Dec 2021 00:19:08: 17000000 INFO @ Sat, 11 Dec 2021 00:19:09: 6000000 INFO @ Sat, 11 Dec 2021 00:19:12: 12000000 INFO @ Sat, 11 Dec 2021 00:19:14: 18000000 INFO @ Sat, 11 Dec 2021 00:19:14: 7000000 INFO @ Sat, 11 Dec 2021 00:19:17: 13000000 INFO @ Sat, 11 Dec 2021 00:19:19: 19000000 INFO @ Sat, 11 Dec 2021 00:19:20: 8000000 INFO @ Sat, 11 Dec 2021 00:19:23: 14000000 INFO @ Sat, 11 Dec 2021 00:19:24: 20000000 INFO @ Sat, 11 Dec 2021 00:19:25: 9000000 INFO @ Sat, 11 Dec 2021 00:19:28: 15000000 INFO @ Sat, 11 Dec 2021 00:19:30: 21000000 INFO @ Sat, 11 Dec 2021 00:19:30: 10000000 INFO @ Sat, 11 Dec 2021 00:19:33: 16000000 INFO @ Sat, 11 Dec 2021 00:19:35: 22000000 INFO @ Sat, 11 Dec 2021 00:19:36: 11000000 INFO @ Sat, 11 Dec 2021 00:19:39: 17000000 INFO @ Sat, 11 Dec 2021 00:19:41: 23000000 INFO @ Sat, 11 Dec 2021 00:19:41: 12000000 INFO @ Sat, 11 Dec 2021 00:19:44: 18000000 INFO @ Sat, 11 Dec 2021 00:19:46: 24000000 INFO @ Sat, 11 Dec 2021 00:19:47: 13000000 INFO @ Sat, 11 Dec 2021 00:19:50: 19000000 INFO @ Sat, 11 Dec 2021 00:19:52: 25000000 INFO @ Sat, 11 Dec 2021 00:19:52: 14000000 INFO @ Sat, 11 Dec 2021 00:19:55: 20000000 INFO @ Sat, 11 Dec 2021 00:19:57: 15000000 INFO @ Sat, 11 Dec 2021 00:19:57: 26000000 INFO @ Sat, 11 Dec 2021 00:20:00: 21000000 INFO @ Sat, 11 Dec 2021 00:20:03: 16000000 INFO @ Sat, 11 Dec 2021 00:20:03: 27000000 INFO @ Sat, 11 Dec 2021 00:20:06: 22000000 INFO @ Sat, 11 Dec 2021 00:20:08: 17000000 INFO @ Sat, 11 Dec 2021 00:20:09: 28000000 INFO @ Sat, 11 Dec 2021 00:20:12: 23000000 INFO @ Sat, 11 Dec 2021 00:20:13: 18000000 INFO @ Sat, 11 Dec 2021 00:20:15: 29000000 INFO @ Sat, 11 Dec 2021 00:20:17: 24000000 INFO @ Sat, 11 Dec 2021 00:20:19: 19000000 INFO @ Sat, 11 Dec 2021 00:20:21: 30000000 INFO @ Sat, 11 Dec 2021 00:20:23: 25000000 INFO @ Sat, 11 Dec 2021 00:20:24: 20000000 INFO @ Sat, 11 Dec 2021 00:20:27: 31000000 INFO @ Sat, 11 Dec 2021 00:20:28: 26000000 INFO @ Sat, 11 Dec 2021 00:20:29: 21000000 INFO @ Sat, 11 Dec 2021 00:20:32: 32000000 INFO @ Sat, 11 Dec 2021 00:20:34: 27000000 INFO @ Sat, 11 Dec 2021 00:20:35: 22000000 INFO @ Sat, 11 Dec 2021 00:20:38: 33000000 INFO @ Sat, 11 Dec 2021 00:20:40: 28000000 INFO @ Sat, 11 Dec 2021 00:20:40: 23000000 INFO @ Sat, 11 Dec 2021 00:20:44: 34000000 INFO @ Sat, 11 Dec 2021 00:20:46: 29000000 INFO @ Sat, 11 Dec 2021 00:20:46: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:20:50: 35000000 INFO @ Sat, 11 Dec 2021 00:20:52: 25000000 INFO @ Sat, 11 Dec 2021 00:20:52: 30000000 INFO @ Sat, 11 Dec 2021 00:20:56: 36000000 INFO @ Sat, 11 Dec 2021 00:20:57: 26000000 INFO @ Sat, 11 Dec 2021 00:20:58: 31000000 INFO @ Sat, 11 Dec 2021 00:21:01: 37000000 INFO @ Sat, 11 Dec 2021 00:21:03: 27000000 INFO @ Sat, 11 Dec 2021 00:21:04: 32000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:21:07: 38000000 INFO @ Sat, 11 Dec 2021 00:21:09: 28000000 INFO @ Sat, 11 Dec 2021 00:21:10: 33000000 INFO @ Sat, 11 Dec 2021 00:21:12: 39000000 INFO @ Sat, 11 Dec 2021 00:21:15: 29000000 INFO @ Sat, 11 Dec 2021 00:21:16: 34000000 INFO @ Sat, 11 Dec 2021 00:21:18: 40000000 INFO @ Sat, 11 Dec 2021 00:21:21: 30000000 INFO @ Sat, 11 Dec 2021 00:21:22: 35000000 INFO @ Sat, 11 Dec 2021 00:21:23: 41000000 INFO @ Sat, 11 Dec 2021 00:21:27: 31000000 INFO @ Sat, 11 Dec 2021 00:21:27: 36000000 INFO @ Sat, 11 Dec 2021 00:21:29: 42000000 INFO @ Sat, 11 Dec 2021 00:21:30: #1 tag size is determined as 80 bps INFO @ Sat, 11 Dec 2021 00:21:30: #1 tag size = 80 INFO @ Sat, 11 Dec 2021 00:21:30: #1 total tags in treatment: 4701453 INFO @ Sat, 11 Dec 2021 00:21:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:21:30: #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 00:21:30: #1 tags after filtering in treatment: 3480319 INFO @ Sat, 11 Dec 2021 00:21:30: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 00:21:30: #1 finished! INFO @ Sat, 11 Dec 2021 00:21:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:21:31: #2 number of paired peaks: 7574 INFO @ Sat, 11 Dec 2021 00:21:31: start model_add_line... INFO @ Sat, 11 Dec 2021 00:21:31: start X-correlation... INFO @ Sat, 11 Dec 2021 00:21:31: end of X-cor INFO @ Sat, 11 Dec 2021 00:21:31: #2 finished! INFO @ Sat, 11 Dec 2021 00:21:31: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 00:21:31: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 00:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.05_model.r INFO @ Sat, 11 Dec 2021 00:21:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:21:33: 32000000 INFO @ Sat, 11 Dec 2021 00:21:33: 37000000 INFO @ Sat, 11 Dec 2021 00:21:38: 33000000 INFO @ Sat, 11 Dec 2021 00:21:38: 38000000 INFO @ Sat, 11 Dec 2021 00:21:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.05_summits.bed INFO @ Sat, 11 Dec 2021 00:21:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11611 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:21:44: 39000000 INFO @ Sat, 11 Dec 2021 00:21:44: 34000000 INFO @ Sat, 11 Dec 2021 00:21:50: 40000000 INFO @ Sat, 11 Dec 2021 00:21:50: 35000000 INFO @ Sat, 11 Dec 2021 00:21:55: 41000000 INFO @ Sat, 11 Dec 2021 00:21:56: 36000000 INFO @ Sat, 11 Dec 2021 00:22:00: 42000000 INFO @ Sat, 11 Dec 2021 00:22:01: 37000000 INFO @ Sat, 11 Dec 2021 00:22:02: #1 tag size is determined as 80 bps INFO @ Sat, 11 Dec 2021 00:22:02: #1 tag size = 80 INFO @ Sat, 11 Dec 2021 00:22:02: #1 total tags in treatment: 4701453 INFO @ Sat, 11 Dec 2021 00:22:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:22:02: #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 00:22:02: #1 tags after filtering in treatment: 3480319 INFO @ Sat, 11 Dec 2021 00:22:02: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 00:22:02: #1 finished! INFO @ Sat, 11 Dec 2021 00:22:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:22:03: #2 number of paired peaks: 7574 INFO @ Sat, 11 Dec 2021 00:22:03: start model_add_line... INFO @ Sat, 11 Dec 2021 00:22:03: start X-correlation... INFO @ Sat, 11 Dec 2021 00:22:03: end of X-cor INFO @ Sat, 11 Dec 2021 00:22:03: #2 finished! INFO @ Sat, 11 Dec 2021 00:22:03: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 00:22:03: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 00:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.10_model.r INFO @ Sat, 11 Dec 2021 00:22:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:22:07: 38000000 INFO @ Sat, 11 Dec 2021 00:22:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:22:12: 39000000 INFO @ Sat, 11 Dec 2021 00:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:22:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.10_summits.bed INFO @ Sat, 11 Dec 2021 00:22:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7976 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:22:17: 40000000 INFO @ Sat, 11 Dec 2021 00:22:23: 41000000 INFO @ Sat, 11 Dec 2021 00:22:28: 42000000 INFO @ Sat, 11 Dec 2021 00:22:29: #1 tag size is determined as 80 bps INFO @ Sat, 11 Dec 2021 00:22:29: #1 tag size = 80 INFO @ Sat, 11 Dec 2021 00:22:29: #1 total tags in treatment: 4701453 INFO @ Sat, 11 Dec 2021 00:22:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:22:29: #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 00:22:30: #1 tags after filtering in treatment: 3480319 INFO @ Sat, 11 Dec 2021 00:22:30: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 00:22:30: #1 finished! INFO @ Sat, 11 Dec 2021 00:22:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:22:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:22:30: #2 number of paired peaks: 7574 INFO @ Sat, 11 Dec 2021 00:22:30: start model_add_line... INFO @ Sat, 11 Dec 2021 00:22:30: start X-correlation... INFO @ Sat, 11 Dec 2021 00:22:30: end of X-cor INFO @ Sat, 11 Dec 2021 00:22:30: #2 finished! INFO @ Sat, 11 Dec 2021 00:22:30: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 00:22:30: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 00:22:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.20_model.r INFO @ Sat, 11 Dec 2021 00:22:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:22:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:22:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978841/ERX3978841.20_summits.bed INFO @ Sat, 11 Dec 2021 00:22:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3915 records, 4 fields): 5 millis CompletedMACS2peakCalling