Job ID = 10166276 SRX = SRX9047374 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22968059 spots for SRR12558902/SRR12558902.sra Written 22968059 spots for SRR12558902/SRR12558902.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166889 ("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: 00:34:06 22968059 reads; of these: 22968059 (100.00%) were paired; of these: 4453458 (19.39%) aligned concordantly 0 times 14258508 (62.08%) aligned concordantly exactly 1 time 4256093 (18.53%) aligned concordantly >1 times ---- 4453458 pairs aligned concordantly 0 times; of these: 1264427 (28.39%) aligned discordantly 1 time ---- 3189031 pairs aligned 0 times concordantly or discordantly; of these: 6378062 mates make up the pairs; of these: 4283850 (67.17%) aligned 0 times 867295 (13.60%) aligned exactly 1 time 1226917 (19.24%) aligned >1 times 90.67% overall alignment rate Time searching: 00:34:06 Overall time: 00:34:06 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] 2075291 / 19744853 = 0.1051 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 21:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.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 @ Thu, 08 Oct 2020 21:30:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:30:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:30:22: 1000000 INFO @ Thu, 08 Oct 2020 21:30:26: 2000000 INFO @ Thu, 08 Oct 2020 21:30:30: 3000000 INFO @ Thu, 08 Oct 2020 21:30:34: 4000000 INFO @ Thu, 08 Oct 2020 21:30:39: 5000000 INFO @ Thu, 08 Oct 2020 21:30:43: 6000000 INFO @ Thu, 08 Oct 2020 21:30:47: 7000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 21:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.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 @ Thu, 08 Oct 2020 21:30:48: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:30:48: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:30:51: 8000000 INFO @ Thu, 08 Oct 2020 21:30:53: 1000000 INFO @ Thu, 08 Oct 2020 21:30:55: 9000000 INFO @ Thu, 08 Oct 2020 21:30:57: 2000000 INFO @ Thu, 08 Oct 2020 21:30:59: 10000000 INFO @ Thu, 08 Oct 2020 21:31:01: 3000000 INFO @ Thu, 08 Oct 2020 21:31:03: 11000000 INFO @ Thu, 08 Oct 2020 21:31:05: 4000000 INFO @ Thu, 08 Oct 2020 21:31:07: 12000000 INFO @ Thu, 08 Oct 2020 21:31:09: 5000000 INFO @ Thu, 08 Oct 2020 21:31:12: 13000000 INFO @ Thu, 08 Oct 2020 21:31:13: 6000000 INFO @ Thu, 08 Oct 2020 21:31:16: 14000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 21:31:18: 7000000 INFO @ Thu, 08 Oct 2020 21:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.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 @ Thu, 08 Oct 2020 21:31:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:31:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:31:20: 15000000 INFO @ Thu, 08 Oct 2020 21:31:22: 8000000 INFO @ Thu, 08 Oct 2020 21:31:23: 1000000 INFO @ Thu, 08 Oct 2020 21:31:24: 16000000 INFO @ Thu, 08 Oct 2020 21:31:26: 9000000 INFO @ Thu, 08 Oct 2020 21:31:27: 2000000 INFO @ Thu, 08 Oct 2020 21:31:28: 17000000 INFO @ Thu, 08 Oct 2020 21:31:30: 10000000 INFO @ Thu, 08 Oct 2020 21:31:31: 3000000 INFO @ Thu, 08 Oct 2020 21:31:33: 18000000 INFO @ Thu, 08 Oct 2020 21:31:34: 11000000 INFO @ Thu, 08 Oct 2020 21:31:35: 4000000 INFO @ Thu, 08 Oct 2020 21:31:37: 19000000 INFO @ Thu, 08 Oct 2020 21:31:39: 12000000 INFO @ Thu, 08 Oct 2020 21:31:40: 5000000 INFO @ Thu, 08 Oct 2020 21:31:41: 20000000 INFO @ Thu, 08 Oct 2020 21:31:43: 13000000 INFO @ Thu, 08 Oct 2020 21:31:44: 6000000 INFO @ Thu, 08 Oct 2020 21:31:45: 21000000 INFO @ Thu, 08 Oct 2020 21:31:47: 14000000 INFO @ Thu, 08 Oct 2020 21:31:48: 7000000 INFO @ Thu, 08 Oct 2020 21:31:49: 22000000 INFO @ Thu, 08 Oct 2020 21:31:51: 15000000 INFO @ Thu, 08 Oct 2020 21:31:52: 8000000 INFO @ Thu, 08 Oct 2020 21:31:54: 23000000 INFO @ Thu, 08 Oct 2020 21:31:55: 16000000 INFO @ Thu, 08 Oct 2020 21:31:56: 9000000 INFO @ Thu, 08 Oct 2020 21:31:58: 24000000 INFO @ Thu, 08 Oct 2020 21:32:00: 17000000 INFO @ Thu, 08 Oct 2020 21:32:01: 10000000 INFO @ Thu, 08 Oct 2020 21:32:02: 25000000 INFO @ Thu, 08 Oct 2020 21:32:04: 18000000 INFO @ Thu, 08 Oct 2020 21:32:05: 11000000 INFO @ Thu, 08 Oct 2020 21:32:06: 26000000 INFO @ Thu, 08 Oct 2020 21:32:08: 19000000 INFO @ Thu, 08 Oct 2020 21:32:09: 12000000 INFO @ Thu, 08 Oct 2020 21:32:10: 27000000 INFO @ Thu, 08 Oct 2020 21:32:12: 20000000 INFO @ Thu, 08 Oct 2020 21:32:13: 13000000 INFO @ Thu, 08 Oct 2020 21:32:14: 28000000 INFO @ Thu, 08 Oct 2020 21:32:16: 21000000 INFO @ Thu, 08 Oct 2020 21:32:18: 14000000 INFO @ Thu, 08 Oct 2020 21:32:19: 29000000 INFO @ Thu, 08 Oct 2020 21:32:21: 22000000 INFO @ Thu, 08 Oct 2020 21:32:22: 15000000 INFO @ Thu, 08 Oct 2020 21:32:23: 30000000 INFO @ Thu, 08 Oct 2020 21:32:25: 23000000 INFO @ Thu, 08 Oct 2020 21:32:26: 16000000 INFO @ Thu, 08 Oct 2020 21:32:27: 31000000 INFO @ Thu, 08 Oct 2020 21:32:29: 24000000 INFO @ Thu, 08 Oct 2020 21:32:30: 17000000 INFO @ Thu, 08 Oct 2020 21:32:31: 32000000 INFO @ Thu, 08 Oct 2020 21:32:33: 25000000 INFO @ Thu, 08 Oct 2020 21:32:34: 18000000 INFO @ Thu, 08 Oct 2020 21:32:35: 33000000 INFO @ Thu, 08 Oct 2020 21:32:37: 26000000 INFO @ Thu, 08 Oct 2020 21:32:39: 19000000 INFO @ Thu, 08 Oct 2020 21:32:40: 34000000 INFO @ Thu, 08 Oct 2020 21:32:41: 27000000 INFO @ Thu, 08 Oct 2020 21:32:43: 20000000 INFO @ Thu, 08 Oct 2020 21:32:44: 35000000 INFO @ Thu, 08 Oct 2020 21:32:46: 28000000 INFO @ Thu, 08 Oct 2020 21:32:47: 21000000 INFO @ Thu, 08 Oct 2020 21:32:48: 36000000 INFO @ Thu, 08 Oct 2020 21:32:50: 29000000 INFO @ Thu, 08 Oct 2020 21:32:51: 22000000 INFO @ Thu, 08 Oct 2020 21:32:52: 37000000 INFO @ Thu, 08 Oct 2020 21:32:54: 30000000 INFO @ Thu, 08 Oct 2020 21:32:54: #1 tag size is determined as 42 bps INFO @ Thu, 08 Oct 2020 21:32:54: #1 tag size = 42 INFO @ Thu, 08 Oct 2020 21:32:54: #1 total tags in treatment: 16517649 INFO @ Thu, 08 Oct 2020 21:32:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:32:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:32:55: #1 tags after filtering in treatment: 12640160 INFO @ Thu, 08 Oct 2020 21:32:55: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 08 Oct 2020 21:32:55: #1 finished! INFO @ Thu, 08 Oct 2020 21:32:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:32:56: 23000000 INFO @ Thu, 08 Oct 2020 21:32:56: #2 number of paired peaks: 2698 INFO @ Thu, 08 Oct 2020 21:32:56: start model_add_line... INFO @ Thu, 08 Oct 2020 21:32:56: start X-correlation... INFO @ Thu, 08 Oct 2020 21:32:56: end of X-cor INFO @ Thu, 08 Oct 2020 21:32:56: #2 finished! INFO @ Thu, 08 Oct 2020 21:32:56: #2 predicted fragment length is 269 bps INFO @ Thu, 08 Oct 2020 21:32:56: #2 alternative fragment length(s) may be 269 bps INFO @ Thu, 08 Oct 2020 21:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.05_model.r INFO @ Thu, 08 Oct 2020 21:32:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:32:58: 31000000 INFO @ Thu, 08 Oct 2020 21:33:00: 24000000 INFO @ Thu, 08 Oct 2020 21:33:02: 32000000 INFO @ Thu, 08 Oct 2020 21:33:04: 25000000 INFO @ Thu, 08 Oct 2020 21:33:07: 33000000 INFO @ Thu, 08 Oct 2020 21:33:08: 26000000 INFO @ Thu, 08 Oct 2020 21:33:11: 34000000 INFO @ Thu, 08 Oct 2020 21:33:12: 27000000 INFO @ Thu, 08 Oct 2020 21:33:15: 35000000 INFO @ Thu, 08 Oct 2020 21:33:16: 28000000 INFO @ Thu, 08 Oct 2020 21:33:19: 36000000 INFO @ Thu, 08 Oct 2020 21:33:21: 29000000 INFO @ Thu, 08 Oct 2020 21:33:23: 37000000 INFO @ Thu, 08 Oct 2020 21:33:25: 30000000 INFO @ Thu, 08 Oct 2020 21:33:25: #1 tag size is determined as 42 bps INFO @ Thu, 08 Oct 2020 21:33:25: #1 tag size = 42 INFO @ Thu, 08 Oct 2020 21:33:25: #1 total tags in treatment: 16517649 INFO @ Thu, 08 Oct 2020 21:33:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:33:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:33:26: #1 tags after filtering in treatment: 12640160 INFO @ Thu, 08 Oct 2020 21:33:26: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 08 Oct 2020 21:33:26: #1 finished! INFO @ Thu, 08 Oct 2020 21:33:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:33:27: #2 number of paired peaks: 2698 INFO @ Thu, 08 Oct 2020 21:33:27: start model_add_line... INFO @ Thu, 08 Oct 2020 21:33:27: start X-correlation... INFO @ Thu, 08 Oct 2020 21:33:27: end of X-cor INFO @ Thu, 08 Oct 2020 21:33:27: #2 finished! INFO @ Thu, 08 Oct 2020 21:33:27: #2 predicted fragment length is 269 bps INFO @ Thu, 08 Oct 2020 21:33:27: #2 alternative fragment length(s) may be 269 bps INFO @ Thu, 08 Oct 2020 21:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.10_model.r INFO @ Thu, 08 Oct 2020 21:33:27: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:33:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:33:29: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:33:33: 32000000 INFO @ Thu, 08 Oct 2020 21:33:37: 33000000 INFO @ Thu, 08 Oct 2020 21:33:41: 34000000 INFO @ Thu, 08 Oct 2020 21:33:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:33:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:33:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.05_summits.bed INFO @ Thu, 08 Oct 2020 21:33:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7473 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:33:45: 35000000 INFO @ Thu, 08 Oct 2020 21:33:49: 36000000 INFO @ Thu, 08 Oct 2020 21:33:53: 37000000 INFO @ Thu, 08 Oct 2020 21:33:56: #1 tag size is determined as 42 bps INFO @ Thu, 08 Oct 2020 21:33:56: #1 tag size = 42 INFO @ Thu, 08 Oct 2020 21:33:56: #1 total tags in treatment: 16517649 INFO @ Thu, 08 Oct 2020 21:33:56: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:33:56: #1 tags after filtering in treatment: 12640160 INFO @ Thu, 08 Oct 2020 21:33:56: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 08 Oct 2020 21:33:56: #1 finished! INFO @ Thu, 08 Oct 2020 21:33:56: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:33:57: #2 number of paired peaks: 2698 INFO @ Thu, 08 Oct 2020 21:33:57: start model_add_line... INFO @ Thu, 08 Oct 2020 21:33:57: start X-correlation... INFO @ Thu, 08 Oct 2020 21:33:57: end of X-cor INFO @ Thu, 08 Oct 2020 21:33:57: #2 finished! INFO @ Thu, 08 Oct 2020 21:33:57: #2 predicted fragment length is 269 bps INFO @ Thu, 08 Oct 2020 21:33:57: #2 alternative fragment length(s) may be 269 bps INFO @ Thu, 08 Oct 2020 21:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.20_model.r INFO @ Thu, 08 Oct 2020 21:33:57: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:33:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:34:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.10_summits.bed INFO @ Thu, 08 Oct 2020 21:34:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5518 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:34:30: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9047374/SRX9047374.20_summits.bed INFO @ Thu, 08 Oct 2020 21:34:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3698 records, 4 fields): 6 millis CompletedMACS2peakCalling