Job ID = 6626565 SRX = SRX7224537 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22519486 spots for SRR10541167/SRR10541167.sra Written 22519486 spots for SRR10541167/SRR10541167.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627144 ("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: 01:49:17 22519486 reads; of these: 22519486 (100.00%) were paired; of these: 2526411 (11.22%) aligned concordantly 0 times 6230790 (27.67%) aligned concordantly exactly 1 time 13762285 (61.11%) aligned concordantly >1 times ---- 2526411 pairs aligned concordantly 0 times; of these: 19845 (0.79%) aligned discordantly 1 time ---- 2506566 pairs aligned 0 times concordantly or discordantly; of these: 5013132 mates make up the pairs; of these: 2844204 (56.74%) aligned 0 times 337286 (6.73%) aligned exactly 1 time 1831642 (36.54%) aligned >1 times 93.69% overall alignment rate Time searching: 01:49:17 Overall time: 01:49:17 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 20 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] 979669 / 19958901 = 0.0491 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 @ Tue, 14 Jul 2020 09:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.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, 14 Jul 2020 09:37:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:37:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:37:34: 1000000 INFO @ Tue, 14 Jul 2020 09:37:41: 2000000 INFO @ Tue, 14 Jul 2020 09:37:48: 3000000 INFO @ Tue, 14 Jul 2020 09:37:54: 4000000 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 @ Tue, 14 Jul 2020 09:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.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, 14 Jul 2020 09:37:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:37:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:38:02: 5000000 INFO @ Tue, 14 Jul 2020 09:38:05: 1000000 INFO @ Tue, 14 Jul 2020 09:38:10: 6000000 INFO @ Tue, 14 Jul 2020 09:38:12: 2000000 INFO @ Tue, 14 Jul 2020 09:38:17: 7000000 INFO @ Tue, 14 Jul 2020 09:38:20: 3000000 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 @ Tue, 14 Jul 2020 09:38:25: 8000000 INFO @ Tue, 14 Jul 2020 09:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.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, 14 Jul 2020 09:38:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:38:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:38:27: 4000000 INFO @ Tue, 14 Jul 2020 09:38:33: 9000000 INFO @ Tue, 14 Jul 2020 09:38:35: 5000000 INFO @ Tue, 14 Jul 2020 09:38:35: 1000000 INFO @ Tue, 14 Jul 2020 09:38:41: 10000000 INFO @ Tue, 14 Jul 2020 09:38:43: 6000000 INFO @ Tue, 14 Jul 2020 09:38:43: 2000000 INFO @ Tue, 14 Jul 2020 09:38:48: 11000000 INFO @ Tue, 14 Jul 2020 09:38:50: 7000000 INFO @ Tue, 14 Jul 2020 09:38:51: 3000000 INFO @ Tue, 14 Jul 2020 09:38:56: 12000000 INFO @ Tue, 14 Jul 2020 09:38:58: 8000000 INFO @ Tue, 14 Jul 2020 09:38:59: 4000000 INFO @ Tue, 14 Jul 2020 09:39:04: 13000000 INFO @ Tue, 14 Jul 2020 09:39:06: 9000000 INFO @ Tue, 14 Jul 2020 09:39:07: 5000000 INFO @ Tue, 14 Jul 2020 09:39:11: 14000000 INFO @ Tue, 14 Jul 2020 09:39:13: 10000000 INFO @ Tue, 14 Jul 2020 09:39:15: 6000000 INFO @ Tue, 14 Jul 2020 09:39:19: 15000000 INFO @ Tue, 14 Jul 2020 09:39:21: 11000000 INFO @ Tue, 14 Jul 2020 09:39:23: 7000000 INFO @ Tue, 14 Jul 2020 09:39:27: 16000000 INFO @ Tue, 14 Jul 2020 09:39:29: 12000000 INFO @ Tue, 14 Jul 2020 09:39:31: 8000000 INFO @ Tue, 14 Jul 2020 09:39:34: 17000000 INFO @ Tue, 14 Jul 2020 09:39:36: 13000000 INFO @ Tue, 14 Jul 2020 09:39:39: 9000000 INFO @ Tue, 14 Jul 2020 09:39:42: 18000000 INFO @ Tue, 14 Jul 2020 09:39:44: 14000000 INFO @ Tue, 14 Jul 2020 09:39:47: 10000000 INFO @ Tue, 14 Jul 2020 09:39:50: 19000000 INFO @ Tue, 14 Jul 2020 09:39:52: 15000000 INFO @ Tue, 14 Jul 2020 09:39:55: 11000000 INFO @ Tue, 14 Jul 2020 09:39:57: 20000000 INFO @ Tue, 14 Jul 2020 09:39:59: 16000000 INFO @ Tue, 14 Jul 2020 09:40:03: 12000000 INFO @ Tue, 14 Jul 2020 09:40:05: 21000000 INFO @ Tue, 14 Jul 2020 09:40:07: 17000000 INFO @ Tue, 14 Jul 2020 09:40:11: 13000000 INFO @ Tue, 14 Jul 2020 09:40:13: 22000000 INFO @ Tue, 14 Jul 2020 09:40:14: 18000000 INFO @ Tue, 14 Jul 2020 09:40:18: 14000000 INFO @ Tue, 14 Jul 2020 09:40:20: 23000000 INFO @ Tue, 14 Jul 2020 09:40:22: 19000000 INFO @ Tue, 14 Jul 2020 09:40:26: 15000000 INFO @ Tue, 14 Jul 2020 09:40:28: 24000000 INFO @ Tue, 14 Jul 2020 09:40:29: 20000000 INFO @ Tue, 14 Jul 2020 09:40:34: 16000000 INFO @ Tue, 14 Jul 2020 09:40:35: 25000000 INFO @ Tue, 14 Jul 2020 09:40:37: 21000000 INFO @ Tue, 14 Jul 2020 09:40:42: 17000000 INFO @ Tue, 14 Jul 2020 09:40:43: 26000000 INFO @ Tue, 14 Jul 2020 09:40:45: 22000000 INFO @ Tue, 14 Jul 2020 09:40:50: 18000000 INFO @ Tue, 14 Jul 2020 09:40:51: 27000000 INFO @ Tue, 14 Jul 2020 09:40:52: 23000000 INFO @ Tue, 14 Jul 2020 09:40:57: 19000000 INFO @ Tue, 14 Jul 2020 09:40:58: 28000000 INFO @ Tue, 14 Jul 2020 09:41:00: 24000000 INFO @ Tue, 14 Jul 2020 09:41:05: 20000000 INFO @ Tue, 14 Jul 2020 09:41:06: 29000000 INFO @ Tue, 14 Jul 2020 09:41:08: 25000000 INFO @ Tue, 14 Jul 2020 09:41:13: 21000000 INFO @ Tue, 14 Jul 2020 09:41:14: 30000000 INFO @ Tue, 14 Jul 2020 09:41:15: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:41:22: 31000000 INFO @ Tue, 14 Jul 2020 09:41:22: 22000000 INFO @ Tue, 14 Jul 2020 09:41:23: 27000000 INFO @ Tue, 14 Jul 2020 09:41:30: 32000000 INFO @ Tue, 14 Jul 2020 09:41:30: 23000000 INFO @ Tue, 14 Jul 2020 09:41:31: 28000000 INFO @ Tue, 14 Jul 2020 09:41:38: 33000000 INFO @ Tue, 14 Jul 2020 09:41:39: 24000000 INFO @ Tue, 14 Jul 2020 09:41:39: 29000000 INFO @ Tue, 14 Jul 2020 09:41:46: 34000000 INFO @ Tue, 14 Jul 2020 09:41:47: 25000000 INFO @ Tue, 14 Jul 2020 09:41:47: 30000000 INFO @ Tue, 14 Jul 2020 09:41:53: 35000000 INFO @ Tue, 14 Jul 2020 09:41:55: 26000000 INFO @ Tue, 14 Jul 2020 09:41:55: 31000000 INFO @ Tue, 14 Jul 2020 09:42:02: 36000000 INFO @ Tue, 14 Jul 2020 09:42:03: 32000000 INFO @ Tue, 14 Jul 2020 09:42:03: 27000000 INFO @ Tue, 14 Jul 2020 09:42:10: 37000000 INFO @ Tue, 14 Jul 2020 09:42:11: 33000000 INFO @ Tue, 14 Jul 2020 09:42:12: 28000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:42:18: 38000000 INFO @ Tue, 14 Jul 2020 09:42:19: 34000000 INFO @ Tue, 14 Jul 2020 09:42:20: 29000000 INFO @ Tue, 14 Jul 2020 09:42:26: 39000000 INFO @ Tue, 14 Jul 2020 09:42:27: 35000000 INFO @ Tue, 14 Jul 2020 09:42:28: 30000000 INFO @ Tue, 14 Jul 2020 09:42:34: 40000000 INFO @ Tue, 14 Jul 2020 09:42:35: 36000000 INFO @ Tue, 14 Jul 2020 09:42:36: #1 tag size is determined as 74 bps INFO @ Tue, 14 Jul 2020 09:42:36: #1 tag size = 74 INFO @ Tue, 14 Jul 2020 09:42:36: #1 total tags in treatment: 19013739 INFO @ Tue, 14 Jul 2020 09:42:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:42:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:42:36: #1 tags after filtering in treatment: 15716920 INFO @ Tue, 14 Jul 2020 09:42:36: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 14 Jul 2020 09:42:36: #1 finished! INFO @ Tue, 14 Jul 2020 09:42:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:42:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:42:37: 31000000 INFO @ Tue, 14 Jul 2020 09:42:38: #2 number of paired peaks: 3935 INFO @ Tue, 14 Jul 2020 09:42:38: start model_add_line... INFO @ Tue, 14 Jul 2020 09:42:38: start X-correlation... INFO @ Tue, 14 Jul 2020 09:42:38: end of X-cor INFO @ Tue, 14 Jul 2020 09:42:38: #2 finished! INFO @ Tue, 14 Jul 2020 09:42:38: #2 predicted fragment length is 171 bps INFO @ Tue, 14 Jul 2020 09:42:38: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 14 Jul 2020 09:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.05_model.r INFO @ Tue, 14 Jul 2020 09:42:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:42:43: 37000000 INFO @ Tue, 14 Jul 2020 09:42:45: 32000000 INFO @ Tue, 14 Jul 2020 09:42:51: 38000000 INFO @ Tue, 14 Jul 2020 09:42:53: 33000000 INFO @ Tue, 14 Jul 2020 09:42:59: 39000000 INFO @ Tue, 14 Jul 2020 09:43:01: 34000000 INFO @ Tue, 14 Jul 2020 09:43:07: 40000000 INFO @ Tue, 14 Jul 2020 09:43:09: #1 tag size is determined as 74 bps INFO @ Tue, 14 Jul 2020 09:43:09: #1 tag size = 74 INFO @ Tue, 14 Jul 2020 09:43:09: #1 total tags in treatment: 19013739 INFO @ Tue, 14 Jul 2020 09:43:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:43:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:43:09: #1 tags after filtering in treatment: 15716920 INFO @ Tue, 14 Jul 2020 09:43:09: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 14 Jul 2020 09:43:09: #1 finished! INFO @ Tue, 14 Jul 2020 09:43:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:43:10: 35000000 INFO @ Tue, 14 Jul 2020 09:43:11: #2 number of paired peaks: 3935 INFO @ Tue, 14 Jul 2020 09:43:11: start model_add_line... INFO @ Tue, 14 Jul 2020 09:43:11: start X-correlation... INFO @ Tue, 14 Jul 2020 09:43:11: end of X-cor INFO @ Tue, 14 Jul 2020 09:43:11: #2 finished! INFO @ Tue, 14 Jul 2020 09:43:11: #2 predicted fragment length is 171 bps INFO @ Tue, 14 Jul 2020 09:43:11: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 14 Jul 2020 09:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.10_model.r INFO @ Tue, 14 Jul 2020 09:43:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:43:17: 36000000 INFO @ Tue, 14 Jul 2020 09:43:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:43:25: 37000000 INFO @ Tue, 14 Jul 2020 09:43:32: 38000000 INFO @ Tue, 14 Jul 2020 09:43:40: 39000000 INFO @ Tue, 14 Jul 2020 09:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.05_summits.bed INFO @ Tue, 14 Jul 2020 09:43:46: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (15418 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:43:48: 40000000 INFO @ Tue, 14 Jul 2020 09:43:50: #1 tag size is determined as 74 bps INFO @ Tue, 14 Jul 2020 09:43:50: #1 tag size = 74 INFO @ Tue, 14 Jul 2020 09:43:50: #1 total tags in treatment: 19013739 INFO @ Tue, 14 Jul 2020 09:43:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:43:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:43:50: #1 tags after filtering in treatment: 15716920 INFO @ Tue, 14 Jul 2020 09:43:50: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 14 Jul 2020 09:43:50: #1 finished! INFO @ Tue, 14 Jul 2020 09:43:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:43:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:43:52: #2 number of paired peaks: 3935 INFO @ Tue, 14 Jul 2020 09:43:52: start model_add_line... INFO @ Tue, 14 Jul 2020 09:43:52: start X-correlation... INFO @ Tue, 14 Jul 2020 09:43:52: end of X-cor INFO @ Tue, 14 Jul 2020 09:43:52: #2 finished! INFO @ Tue, 14 Jul 2020 09:43:52: #2 predicted fragment length is 171 bps INFO @ Tue, 14 Jul 2020 09:43:52: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 14 Jul 2020 09:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.20_model.r INFO @ Tue, 14 Jul 2020 09:43:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:43:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.10_summits.bed INFO @ Tue, 14 Jul 2020 09:44:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9969 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:44:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224537/SRX7224537.20_summits.bed INFO @ Tue, 14 Jul 2020 09:45:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5183 records, 4 fields): 8 millis CompletedMACS2peakCalling