Job ID = 16439649 SRX = SRX11499351 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27106838 spots for SRR15192732/SRR15192732.sra Written 27106838 spots for SRR15192732/SRR15192732.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440091 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:03:43 27106838 reads; of these: 27106838 (100.00%) were paired; of these: 8356184 (30.83%) aligned concordantly 0 times 17319155 (63.89%) aligned concordantly exactly 1 time 1431499 (5.28%) aligned concordantly >1 times ---- 8356184 pairs aligned concordantly 0 times; of these: 2854948 (34.17%) aligned discordantly 1 time ---- 5501236 pairs aligned 0 times concordantly or discordantly; of these: 11002472 mates make up the pairs; of these: 9423363 (85.65%) aligned 0 times 1042892 (9.48%) aligned exactly 1 time 536217 (4.87%) aligned >1 times 82.62% overall alignment rate Time searching: 01:03:44 Overall time: 01:03:44 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 36 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] 2562542 / 20634755 = 0.1242 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.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 @ Tue, 02 Aug 2022 17:29:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:29:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:30:00: 1000000 INFO @ Tue, 02 Aug 2022 17:30:11: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.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 @ Tue, 02 Aug 2022 17:30:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:30:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:30:24: 3000000 INFO @ Tue, 02 Aug 2022 17:30:29: 1000000 INFO @ Tue, 02 Aug 2022 17:30:36: 4000000 INFO @ Tue, 02 Aug 2022 17:30:41: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.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 @ Tue, 02 Aug 2022 17:30:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:30:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:30:49: 5000000 INFO @ Tue, 02 Aug 2022 17:30:54: 3000000 INFO @ Tue, 02 Aug 2022 17:30:58: 1000000 INFO @ Tue, 02 Aug 2022 17:31:02: 6000000 INFO @ Tue, 02 Aug 2022 17:31:05: 4000000 INFO @ Tue, 02 Aug 2022 17:31:10: 2000000 INFO @ Tue, 02 Aug 2022 17:31:12: 7000000 INFO @ Tue, 02 Aug 2022 17:31:16: 5000000 INFO @ Tue, 02 Aug 2022 17:31:22: 3000000 INFO @ Tue, 02 Aug 2022 17:31:23: 8000000 INFO @ Tue, 02 Aug 2022 17:31:27: 6000000 INFO @ Tue, 02 Aug 2022 17:31:34: 4000000 INFO @ Tue, 02 Aug 2022 17:31:34: 9000000 INFO @ Tue, 02 Aug 2022 17:31:38: 7000000 INFO @ Tue, 02 Aug 2022 17:31:46: 10000000 INFO @ Tue, 02 Aug 2022 17:31:46: 5000000 INFO @ Tue, 02 Aug 2022 17:31:49: 8000000 INFO @ Tue, 02 Aug 2022 17:31:56: 11000000 INFO @ Tue, 02 Aug 2022 17:31:58: 6000000 INFO @ Tue, 02 Aug 2022 17:32:00: 9000000 INFO @ Tue, 02 Aug 2022 17:32:08: 12000000 INFO @ Tue, 02 Aug 2022 17:32:11: 7000000 INFO @ Tue, 02 Aug 2022 17:32:11: 10000000 INFO @ Tue, 02 Aug 2022 17:32:18: 13000000 INFO @ Tue, 02 Aug 2022 17:32:22: 11000000 INFO @ Tue, 02 Aug 2022 17:32:23: 8000000 INFO @ Tue, 02 Aug 2022 17:32:29: 14000000 INFO @ Tue, 02 Aug 2022 17:32:33: 12000000 INFO @ Tue, 02 Aug 2022 17:32:35: 9000000 INFO @ Tue, 02 Aug 2022 17:32:39: 15000000 INFO @ Tue, 02 Aug 2022 17:32:43: 13000000 INFO @ Tue, 02 Aug 2022 17:32:47: 10000000 INFO @ Tue, 02 Aug 2022 17:32:49: 16000000 INFO @ Tue, 02 Aug 2022 17:32:54: 14000000 INFO @ Tue, 02 Aug 2022 17:32:59: 11000000 INFO @ Tue, 02 Aug 2022 17:33:00: 17000000 INFO @ Tue, 02 Aug 2022 17:33:05: 15000000 INFO @ Tue, 02 Aug 2022 17:33:11: 12000000 INFO @ Tue, 02 Aug 2022 17:33:11: 18000000 INFO @ Tue, 02 Aug 2022 17:33:15: 16000000 INFO @ Tue, 02 Aug 2022 17:33:22: 19000000 INFO @ Tue, 02 Aug 2022 17:33:22: 13000000 INFO @ Tue, 02 Aug 2022 17:33:26: 17000000 INFO @ Tue, 02 Aug 2022 17:33:32: 20000000 INFO @ Tue, 02 Aug 2022 17:33:34: 14000000 INFO @ Tue, 02 Aug 2022 17:33:36: 18000000 INFO @ Tue, 02 Aug 2022 17:33:43: 21000000 INFO @ Tue, 02 Aug 2022 17:33:45: 15000000 INFO @ Tue, 02 Aug 2022 17:33:47: 19000000 INFO @ Tue, 02 Aug 2022 17:33:54: 22000000 INFO @ Tue, 02 Aug 2022 17:33:57: 16000000 INFO @ Tue, 02 Aug 2022 17:33:58: 20000000 INFO @ Tue, 02 Aug 2022 17:34:04: 23000000 INFO @ Tue, 02 Aug 2022 17:34:08: 21000000 INFO @ Tue, 02 Aug 2022 17:34:09: 17000000 INFO @ Tue, 02 Aug 2022 17:34:15: 24000000 INFO @ Tue, 02 Aug 2022 17:34:20: 22000000 INFO @ Tue, 02 Aug 2022 17:34:21: 18000000 INFO @ Tue, 02 Aug 2022 17:34:27: 25000000 INFO @ Tue, 02 Aug 2022 17:34:31: 23000000 INFO @ Tue, 02 Aug 2022 17:34:33: 19000000 INFO @ Tue, 02 Aug 2022 17:34:39: 26000000 INFO @ Tue, 02 Aug 2022 17:34:44: 24000000 INFO @ Tue, 02 Aug 2022 17:34:45: 20000000 INFO @ Tue, 02 Aug 2022 17:34:51: 27000000 INFO @ Tue, 02 Aug 2022 17:34:55: 25000000 INFO @ Tue, 02 Aug 2022 17:34:57: 21000000 INFO @ Tue, 02 Aug 2022 17:35:02: 28000000 INFO @ Tue, 02 Aug 2022 17:35:06: 26000000 INFO @ Tue, 02 Aug 2022 17:35:09: 22000000 INFO @ Tue, 02 Aug 2022 17:35:13: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:35:17: 27000000 INFO @ Tue, 02 Aug 2022 17:35:21: 23000000 INFO @ Tue, 02 Aug 2022 17:35:23: 30000000 INFO @ Tue, 02 Aug 2022 17:35:28: 28000000 INFO @ Tue, 02 Aug 2022 17:35:33: 24000000 INFO @ Tue, 02 Aug 2022 17:35:36: 31000000 INFO @ Tue, 02 Aug 2022 17:35:40: 29000000 INFO @ Tue, 02 Aug 2022 17:35:45: 25000000 INFO @ Tue, 02 Aug 2022 17:35:47: 32000000 INFO @ Tue, 02 Aug 2022 17:35:51: 30000000 INFO @ Tue, 02 Aug 2022 17:35:56: 26000000 INFO @ Tue, 02 Aug 2022 17:35:59: 33000000 INFO @ Tue, 02 Aug 2022 17:36:03: 31000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:36:08: 27000000 INFO @ Tue, 02 Aug 2022 17:36:12: 34000000 INFO @ Tue, 02 Aug 2022 17:36:15: 32000000 INFO @ Tue, 02 Aug 2022 17:36:20: 28000000 INFO @ Tue, 02 Aug 2022 17:36:25: 35000000 INFO @ Tue, 02 Aug 2022 17:36:27: 33000000 INFO @ Tue, 02 Aug 2022 17:36:32: 29000000 INFO @ Tue, 02 Aug 2022 17:36:37: 36000000 INFO @ Tue, 02 Aug 2022 17:36:39: 34000000 INFO @ Tue, 02 Aug 2022 17:36:44: 30000000 INFO @ Tue, 02 Aug 2022 17:36:50: 37000000 INFO @ Tue, 02 Aug 2022 17:36:51: 35000000 INFO @ Tue, 02 Aug 2022 17:36:56: 31000000 INFO @ Tue, 02 Aug 2022 17:37:02: 38000000 INFO @ Tue, 02 Aug 2022 17:37:03: 36000000 INFO @ Tue, 02 Aug 2022 17:37:08: 32000000 INFO @ Tue, 02 Aug 2022 17:37:14: 39000000 INFO @ Tue, 02 Aug 2022 17:37:15: 37000000 INFO @ Tue, 02 Aug 2022 17:37:22: 33000000 INFO @ Tue, 02 Aug 2022 17:37:22: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:37:22: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:37:22: #1 total tags in treatment: 16404218 INFO @ Tue, 02 Aug 2022 17:37:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:37:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:37:23: #1 tags after filtering in treatment: 9073346 INFO @ Tue, 02 Aug 2022 17:37:23: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 02 Aug 2022 17:37:23: #1 finished! INFO @ Tue, 02 Aug 2022 17:37:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:37:24: #2 number of paired peaks: 7494 INFO @ Tue, 02 Aug 2022 17:37:24: start model_add_line... INFO @ Tue, 02 Aug 2022 17:37:24: start X-correlation... INFO @ Tue, 02 Aug 2022 17:37:25: end of X-cor INFO @ Tue, 02 Aug 2022 17:37:25: #2 finished! INFO @ Tue, 02 Aug 2022 17:37:25: #2 predicted fragment length is 289 bps INFO @ Tue, 02 Aug 2022 17:37:25: #2 alternative fragment length(s) may be 289 bps INFO @ Tue, 02 Aug 2022 17:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.05_model.r INFO @ Tue, 02 Aug 2022 17:37:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:37:26: 38000000 INFO @ Tue, 02 Aug 2022 17:37:35: 34000000 INFO @ Tue, 02 Aug 2022 17:37:37: 39000000 INFO @ Tue, 02 Aug 2022 17:37:45: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:37:45: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:37:45: #1 total tags in treatment: 16404218 INFO @ Tue, 02 Aug 2022 17:37:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:37:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:37:45: #1 tags after filtering in treatment: 9073346 INFO @ Tue, 02 Aug 2022 17:37:45: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 02 Aug 2022 17:37:45: #1 finished! INFO @ Tue, 02 Aug 2022 17:37:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:37:47: #2 number of paired peaks: 7494 INFO @ Tue, 02 Aug 2022 17:37:47: start model_add_line... INFO @ Tue, 02 Aug 2022 17:37:47: start X-correlation... INFO @ Tue, 02 Aug 2022 17:37:47: end of X-cor INFO @ Tue, 02 Aug 2022 17:37:47: #2 finished! INFO @ Tue, 02 Aug 2022 17:37:47: #2 predicted fragment length is 289 bps INFO @ Tue, 02 Aug 2022 17:37:47: #2 alternative fragment length(s) may be 289 bps INFO @ Tue, 02 Aug 2022 17:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.10_model.r INFO @ Tue, 02 Aug 2022 17:37:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:37:47: 35000000 INFO @ Tue, 02 Aug 2022 17:37:59: 36000000 INFO @ Tue, 02 Aug 2022 17:38:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:38:11: 37000000 INFO @ Tue, 02 Aug 2022 17:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.05_summits.bed INFO @ Tue, 02 Aug 2022 17:38:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7151 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:38:24: 38000000 INFO @ Tue, 02 Aug 2022 17:38:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:38:34: 39000000 INFO @ Tue, 02 Aug 2022 17:38:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:38:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:38:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.10_summits.bed INFO @ Tue, 02 Aug 2022 17:38:42: #1 tag size is determined as 144 bps INFO @ Tue, 02 Aug 2022 17:38:42: #1 tag size = 144 INFO @ Tue, 02 Aug 2022 17:38:42: #1 total tags in treatment: 16404218 INFO @ Tue, 02 Aug 2022 17:38:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:38:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:38:42: Done! INFO @ Tue, 02 Aug 2022 17:38:43: #1 tags after filtering in treatment: 9073346 INFO @ Tue, 02 Aug 2022 17:38:43: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 02 Aug 2022 17:38:43: #1 finished! INFO @ Tue, 02 Aug 2022 17:38:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:38:43: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6476 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:38:44: #2 number of paired peaks: 7494 INFO @ Tue, 02 Aug 2022 17:38:44: start model_add_line... INFO @ Tue, 02 Aug 2022 17:38:44: start X-correlation... INFO @ Tue, 02 Aug 2022 17:38:45: end of X-cor INFO @ Tue, 02 Aug 2022 17:38:45: #2 finished! INFO @ Tue, 02 Aug 2022 17:38:45: #2 predicted fragment length is 289 bps INFO @ Tue, 02 Aug 2022 17:38:45: #2 alternative fragment length(s) may be 289 bps INFO @ Tue, 02 Aug 2022 17:38:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.20_model.r INFO @ Tue, 02 Aug 2022 17:38:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:38:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:39:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:39:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:39:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:39:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11499351/SRX11499351.20_summits.bed INFO @ Tue, 02 Aug 2022 17:39:40: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5773 records, 4 fields): 78 millis CompletedMACS2peakCalling