Job ID = 14172451 SRX = SRX7628888 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17933478 spots for SRR10963250/SRR10963250.sra Written 17933478 spots for SRR10963250/SRR10963250.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173063 ("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: 00:52:53 17933478 reads; of these: 17933478 (100.00%) were paired; of these: 867680 (4.84%) aligned concordantly 0 times 10965461 (61.15%) aligned concordantly exactly 1 time 6100337 (34.02%) aligned concordantly >1 times ---- 867680 pairs aligned concordantly 0 times; of these: 80098 (9.23%) aligned discordantly 1 time ---- 787582 pairs aligned 0 times concordantly or discordantly; of these: 1575164 mates make up the pairs; of these: 779892 (49.51%) aligned 0 times 439545 (27.90%) aligned exactly 1 time 355727 (22.58%) aligned >1 times 97.83% overall alignment rate Time searching: 00:52:53 Overall time: 00:52:53 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] 1500324 / 17100163 = 0.0877 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 16:33:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.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 16:33:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:33:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:33:51: 1000000 INFO @ Sat, 11 Dec 2021 16:33:57: 2000000 INFO @ Sat, 11 Dec 2021 16:34:04: 3000000 INFO @ Sat, 11 Dec 2021 16:34:11: 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 16:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.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 16:34:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:34:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:34:18: 5000000 INFO @ Sat, 11 Dec 2021 16:34:23: 1000000 INFO @ Sat, 11 Dec 2021 16:34:25: 6000000 INFO @ Sat, 11 Dec 2021 16:34:31: 7000000 INFO @ Sat, 11 Dec 2021 16:34:33: 2000000 INFO @ Sat, 11 Dec 2021 16:34:39: 8000000 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 16:34:43: 3000000 INFO @ Sat, 11 Dec 2021 16:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.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 16:34:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:34:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:34:45: 9000000 INFO @ Sat, 11 Dec 2021 16:34:52: 10000000 INFO @ Sat, 11 Dec 2021 16:34:53: 4000000 INFO @ Sat, 11 Dec 2021 16:34:54: 1000000 INFO @ Sat, 11 Dec 2021 16:35:00: 11000000 INFO @ Sat, 11 Dec 2021 16:35:03: 5000000 INFO @ Sat, 11 Dec 2021 16:35:04: 2000000 INFO @ Sat, 11 Dec 2021 16:35:07: 12000000 INFO @ Sat, 11 Dec 2021 16:35:14: 3000000 INFO @ Sat, 11 Dec 2021 16:35:14: 6000000 INFO @ Sat, 11 Dec 2021 16:35:15: 13000000 INFO @ Sat, 11 Dec 2021 16:35:22: 14000000 INFO @ Sat, 11 Dec 2021 16:35:23: 7000000 INFO @ Sat, 11 Dec 2021 16:35:24: 4000000 INFO @ Sat, 11 Dec 2021 16:35:29: 15000000 INFO @ Sat, 11 Dec 2021 16:35:33: 5000000 INFO @ Sat, 11 Dec 2021 16:35:34: 8000000 INFO @ Sat, 11 Dec 2021 16:35:36: 16000000 INFO @ Sat, 11 Dec 2021 16:35:43: 6000000 INFO @ Sat, 11 Dec 2021 16:35:43: 17000000 INFO @ Sat, 11 Dec 2021 16:35:43: 9000000 INFO @ Sat, 11 Dec 2021 16:35:50: 18000000 INFO @ Sat, 11 Dec 2021 16:35:53: 7000000 INFO @ Sat, 11 Dec 2021 16:35:53: 10000000 INFO @ Sat, 11 Dec 2021 16:35:57: 19000000 INFO @ Sat, 11 Dec 2021 16:36:03: 8000000 INFO @ Sat, 11 Dec 2021 16:36:03: 11000000 INFO @ Sat, 11 Dec 2021 16:36:04: 20000000 INFO @ Sat, 11 Dec 2021 16:36:12: 21000000 INFO @ Sat, 11 Dec 2021 16:36:12: 9000000 INFO @ Sat, 11 Dec 2021 16:36:14: 12000000 INFO @ Sat, 11 Dec 2021 16:36:19: 22000000 INFO @ Sat, 11 Dec 2021 16:36:23: 10000000 INFO @ Sat, 11 Dec 2021 16:36:24: 13000000 INFO @ Sat, 11 Dec 2021 16:36:26: 23000000 INFO @ Sat, 11 Dec 2021 16:36:32: 11000000 INFO @ Sat, 11 Dec 2021 16:36:33: 24000000 INFO @ Sat, 11 Dec 2021 16:36:33: 14000000 INFO @ Sat, 11 Dec 2021 16:36:40: 25000000 INFO @ Sat, 11 Dec 2021 16:36:42: 12000000 INFO @ Sat, 11 Dec 2021 16:36:43: 15000000 INFO @ Sat, 11 Dec 2021 16:36:48: 26000000 INFO @ Sat, 11 Dec 2021 16:36:52: 13000000 INFO @ Sat, 11 Dec 2021 16:36:53: 16000000 INFO @ Sat, 11 Dec 2021 16:36:54: 27000000 INFO @ Sat, 11 Dec 2021 16:37:01: 28000000 INFO @ Sat, 11 Dec 2021 16:37:02: 14000000 INFO @ Sat, 11 Dec 2021 16:37:02: 17000000 INFO @ Sat, 11 Dec 2021 16:37:08: 29000000 INFO @ Sat, 11 Dec 2021 16:37:12: 18000000 INFO @ Sat, 11 Dec 2021 16:37:12: 15000000 INFO @ Sat, 11 Dec 2021 16:37:16: 30000000 INFO @ Sat, 11 Dec 2021 16:37:21: 19000000 INFO @ Sat, 11 Dec 2021 16:37:21: 16000000 INFO @ Sat, 11 Dec 2021 16:37:23: 31000000 INFO @ Sat, 11 Dec 2021 16:37:30: 32000000 INFO @ Sat, 11 Dec 2021 16:37:31: 17000000 INFO @ Sat, 11 Dec 2021 16:37:31: 20000000 INFO @ Sat, 11 Dec 2021 16:37:31: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:37:31: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:37:31: #1 total tags in treatment: 15566113 INFO @ Sat, 11 Dec 2021 16:37:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:37:31: #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 16:37:31: #1 tags after filtering in treatment: 14168524 INFO @ Sat, 11 Dec 2021 16:37:31: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 16:37:31: #1 finished! INFO @ Sat, 11 Dec 2021 16:37:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:37:33: #2 number of paired peaks: 1202 INFO @ Sat, 11 Dec 2021 16:37:33: start model_add_line... INFO @ Sat, 11 Dec 2021 16:37:33: start X-correlation... INFO @ Sat, 11 Dec 2021 16:37:33: end of X-cor INFO @ Sat, 11 Dec 2021 16:37:33: #2 finished! INFO @ Sat, 11 Dec 2021 16:37:33: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 16:37:33: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sat, 11 Dec 2021 16:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.05_model.r INFO @ Sat, 11 Dec 2021 16:37:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:37:40: 18000000 INFO @ Sat, 11 Dec 2021 16:37:40: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:37:49: 19000000 INFO @ Sat, 11 Dec 2021 16:37:50: 22000000 INFO @ Sat, 11 Dec 2021 16:37:58: 20000000 INFO @ Sat, 11 Dec 2021 16:37:59: 23000000 INFO @ Sat, 11 Dec 2021 16:38:07: 21000000 INFO @ Sat, 11 Dec 2021 16:38:09: 24000000 INFO @ Sat, 11 Dec 2021 16:38:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:38:17: 22000000 INFO @ Sat, 11 Dec 2021 16:38:18: 25000000 INFO @ Sat, 11 Dec 2021 16:38:26: 23000000 INFO @ Sat, 11 Dec 2021 16:38:28: 26000000 INFO @ Sat, 11 Dec 2021 16:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.05_summits.bed INFO @ Sat, 11 Dec 2021 16:38:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2931 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:38:35: 24000000 INFO @ Sat, 11 Dec 2021 16:38:37: 27000000 INFO @ Sat, 11 Dec 2021 16:38:44: 25000000 INFO @ Sat, 11 Dec 2021 16:38:46: 28000000 INFO @ Sat, 11 Dec 2021 16:38:54: 26000000 INFO @ Sat, 11 Dec 2021 16:38:55: 29000000 INFO @ Sat, 11 Dec 2021 16:39:03: 27000000 INFO @ Sat, 11 Dec 2021 16:39:05: 30000000 INFO @ Sat, 11 Dec 2021 16:39:12: 28000000 INFO @ Sat, 11 Dec 2021 16:39:14: 31000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:39:21: 29000000 INFO @ Sat, 11 Dec 2021 16:39:23: 32000000 INFO @ Sat, 11 Dec 2021 16:39:24: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:39:24: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:39:24: #1 total tags in treatment: 15566113 INFO @ Sat, 11 Dec 2021 16:39:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:39:24: #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 16:39:24: #1 tags after filtering in treatment: 14168524 INFO @ Sat, 11 Dec 2021 16:39:24: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 16:39:24: #1 finished! INFO @ Sat, 11 Dec 2021 16:39:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:39:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:39:26: #2 number of paired peaks: 1202 INFO @ Sat, 11 Dec 2021 16:39:26: start model_add_line... INFO @ Sat, 11 Dec 2021 16:39:26: start X-correlation... INFO @ Sat, 11 Dec 2021 16:39:26: end of X-cor INFO @ Sat, 11 Dec 2021 16:39:26: #2 finished! INFO @ Sat, 11 Dec 2021 16:39:26: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 16:39:26: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sat, 11 Dec 2021 16:39:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.10_model.r INFO @ Sat, 11 Dec 2021 16:39:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:39:30: 30000000 INFO @ Sat, 11 Dec 2021 16:39:39: 31000000 INFO @ Sat, 11 Dec 2021 16:39:48: 32000000 INFO @ Sat, 11 Dec 2021 16:39:49: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 16:39:49: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 16:39:49: #1 total tags in treatment: 15566113 INFO @ Sat, 11 Dec 2021 16:39:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:39:49: #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 16:39:49: #1 tags after filtering in treatment: 14168524 INFO @ Sat, 11 Dec 2021 16:39:49: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 16:39:49: #1 finished! INFO @ Sat, 11 Dec 2021 16:39:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:39:51: #2 number of paired peaks: 1202 INFO @ Sat, 11 Dec 2021 16:39:51: start model_add_line... INFO @ Sat, 11 Dec 2021 16:39:51: start X-correlation... INFO @ Sat, 11 Dec 2021 16:39:51: end of X-cor INFO @ Sat, 11 Dec 2021 16:39:51: #2 finished! INFO @ Sat, 11 Dec 2021 16:39:51: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 16:39:51: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sat, 11 Dec 2021 16:39:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.20_model.r INFO @ Sat, 11 Dec 2021 16:39:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:40:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:40:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:40:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:40:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.10_summits.bed INFO @ Sat, 11 Dec 2021 16:40:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1888 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:40:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628888/SRX7628888.20_summits.bed INFO @ Sat, 11 Dec 2021 16:40:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1097 records, 4 fields): 7 millis CompletedMACS2peakCalling