Job ID = 6626481 SRX = SRX5736463 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21480267 spots for SRR8956875/SRR8956875.sra Written 21480267 spots for SRR8956875/SRR8956875.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626792 ("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: 01:09:01 21480267 reads; of these: 21480267 (100.00%) were paired; of these: 3071054 (14.30%) aligned concordantly 0 times 10099519 (47.02%) aligned concordantly exactly 1 time 8309694 (38.69%) aligned concordantly >1 times ---- 3071054 pairs aligned concordantly 0 times; of these: 494673 (16.11%) aligned discordantly 1 time ---- 2576381 pairs aligned 0 times concordantly or discordantly; of these: 5152762 mates make up the pairs; of these: 3620807 (70.27%) aligned 0 times 456583 (8.86%) aligned exactly 1 time 1075372 (20.87%) aligned >1 times 91.57% overall alignment rate Time searching: 01:09:01 Overall time: 01:09:01 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] 1333032 / 18796606 = 0.0709 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 08:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.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 08:29:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:29:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:29:11: 1000000 INFO @ Tue, 14 Jul 2020 08:29:18: 2000000 INFO @ Tue, 14 Jul 2020 08:29:24: 3000000 INFO @ Tue, 14 Jul 2020 08:29:31: 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 08:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.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 08:29:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:29:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:29:37: 5000000 INFO @ Tue, 14 Jul 2020 08:29:42: 1000000 INFO @ Tue, 14 Jul 2020 08:29:44: 6000000 INFO @ Tue, 14 Jul 2020 08:29:49: 2000000 INFO @ Tue, 14 Jul 2020 08:29:51: 7000000 INFO @ Tue, 14 Jul 2020 08:29:56: 3000000 INFO @ Tue, 14 Jul 2020 08:29:59: 8000000 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 08:30:03: 4000000 INFO @ Tue, 14 Jul 2020 08:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.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 08:30:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:30:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:30:06: 9000000 INFO @ Tue, 14 Jul 2020 08:30:11: 5000000 INFO @ Tue, 14 Jul 2020 08:30:12: 1000000 INFO @ Tue, 14 Jul 2020 08:30:13: 10000000 INFO @ Tue, 14 Jul 2020 08:30:18: 6000000 INFO @ Tue, 14 Jul 2020 08:30:20: 2000000 INFO @ Tue, 14 Jul 2020 08:30:20: 11000000 INFO @ Tue, 14 Jul 2020 08:30:25: 7000000 INFO @ Tue, 14 Jul 2020 08:30:27: 3000000 INFO @ Tue, 14 Jul 2020 08:30:27: 12000000 INFO @ Tue, 14 Jul 2020 08:30:32: 8000000 INFO @ Tue, 14 Jul 2020 08:30:34: 4000000 INFO @ Tue, 14 Jul 2020 08:30:34: 13000000 INFO @ Tue, 14 Jul 2020 08:30:40: 9000000 INFO @ Tue, 14 Jul 2020 08:30:41: 5000000 INFO @ Tue, 14 Jul 2020 08:30:41: 14000000 INFO @ Tue, 14 Jul 2020 08:30:47: 10000000 INFO @ Tue, 14 Jul 2020 08:30:48: 6000000 INFO @ Tue, 14 Jul 2020 08:30:48: 15000000 INFO @ Tue, 14 Jul 2020 08:30:54: 11000000 INFO @ Tue, 14 Jul 2020 08:30:55: 16000000 INFO @ Tue, 14 Jul 2020 08:30:55: 7000000 INFO @ Tue, 14 Jul 2020 08:31:01: 12000000 INFO @ Tue, 14 Jul 2020 08:31:02: 17000000 INFO @ Tue, 14 Jul 2020 08:31:03: 8000000 INFO @ Tue, 14 Jul 2020 08:31:08: 13000000 INFO @ Tue, 14 Jul 2020 08:31:09: 18000000 INFO @ Tue, 14 Jul 2020 08:31:10: 9000000 INFO @ Tue, 14 Jul 2020 08:31:15: 14000000 INFO @ Tue, 14 Jul 2020 08:31:16: 19000000 INFO @ Tue, 14 Jul 2020 08:31:17: 10000000 INFO @ Tue, 14 Jul 2020 08:31:22: 15000000 INFO @ Tue, 14 Jul 2020 08:31:23: 20000000 INFO @ Tue, 14 Jul 2020 08:31:24: 11000000 INFO @ Tue, 14 Jul 2020 08:31:29: 16000000 INFO @ Tue, 14 Jul 2020 08:31:30: 21000000 INFO @ Tue, 14 Jul 2020 08:31:31: 12000000 INFO @ Tue, 14 Jul 2020 08:31:36: 17000000 INFO @ Tue, 14 Jul 2020 08:31:37: 22000000 INFO @ Tue, 14 Jul 2020 08:31:38: 13000000 INFO @ Tue, 14 Jul 2020 08:31:44: 18000000 INFO @ Tue, 14 Jul 2020 08:31:44: 23000000 INFO @ Tue, 14 Jul 2020 08:31:45: 14000000 INFO @ Tue, 14 Jul 2020 08:31:51: 19000000 INFO @ Tue, 14 Jul 2020 08:31:52: 24000000 INFO @ Tue, 14 Jul 2020 08:31:52: 15000000 INFO @ Tue, 14 Jul 2020 08:31:58: 20000000 INFO @ Tue, 14 Jul 2020 08:31:59: 25000000 INFO @ Tue, 14 Jul 2020 08:31:59: 16000000 INFO @ Tue, 14 Jul 2020 08:32:05: 21000000 INFO @ Tue, 14 Jul 2020 08:32:06: 26000000 INFO @ Tue, 14 Jul 2020 08:32:06: 17000000 INFO @ Tue, 14 Jul 2020 08:32:12: 22000000 INFO @ Tue, 14 Jul 2020 08:32:13: 27000000 INFO @ Tue, 14 Jul 2020 08:32:14: 18000000 INFO @ Tue, 14 Jul 2020 08:32:19: 23000000 INFO @ Tue, 14 Jul 2020 08:32:20: 28000000 INFO @ Tue, 14 Jul 2020 08:32:21: 19000000 INFO @ Tue, 14 Jul 2020 08:32:26: 24000000 INFO @ Tue, 14 Jul 2020 08:32:27: 29000000 INFO @ Tue, 14 Jul 2020 08:32:28: 20000000 INFO @ Tue, 14 Jul 2020 08:32:33: 25000000 INFO @ Tue, 14 Jul 2020 08:32:34: 30000000 INFO @ Tue, 14 Jul 2020 08:32:35: 21000000 INFO @ Tue, 14 Jul 2020 08:32:40: 26000000 INFO @ Tue, 14 Jul 2020 08:32:41: 31000000 INFO @ Tue, 14 Jul 2020 08:32:42: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:32:47: 27000000 INFO @ Tue, 14 Jul 2020 08:32:48: 32000000 INFO @ Tue, 14 Jul 2020 08:32:49: 23000000 INFO @ Tue, 14 Jul 2020 08:32:54: 28000000 INFO @ Tue, 14 Jul 2020 08:32:55: 33000000 INFO @ Tue, 14 Jul 2020 08:32:56: 24000000 INFO @ Tue, 14 Jul 2020 08:33:02: 29000000 INFO @ Tue, 14 Jul 2020 08:33:02: 34000000 INFO @ Tue, 14 Jul 2020 08:33:03: 25000000 INFO @ Tue, 14 Jul 2020 08:33:09: 30000000 INFO @ Tue, 14 Jul 2020 08:33:09: 35000000 INFO @ Tue, 14 Jul 2020 08:33:10: 26000000 INFO @ Tue, 14 Jul 2020 08:33:16: 31000000 INFO @ Tue, 14 Jul 2020 08:33:16: 36000000 INFO @ Tue, 14 Jul 2020 08:33:17: 27000000 INFO @ Tue, 14 Jul 2020 08:33:21: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:33:21: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:33:21: #1 total tags in treatment: 17083939 INFO @ Tue, 14 Jul 2020 08:33:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:33:21: #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 08:33:21: #1 tags after filtering in treatment: 15173357 INFO @ Tue, 14 Jul 2020 08:33:21: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 08:33:21: #1 finished! INFO @ Tue, 14 Jul 2020 08:33:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:33:22: #2 number of paired peaks: 128 WARNING @ Tue, 14 Jul 2020 08:33:22: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 14 Jul 2020 08:33:22: start model_add_line... INFO @ Tue, 14 Jul 2020 08:33:22: start X-correlation... INFO @ Tue, 14 Jul 2020 08:33:22: end of X-cor INFO @ Tue, 14 Jul 2020 08:33:22: #2 finished! INFO @ Tue, 14 Jul 2020 08:33:22: #2 predicted fragment length is 160 bps INFO @ Tue, 14 Jul 2020 08:33:22: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 14 Jul 2020 08:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.05_model.r INFO @ Tue, 14 Jul 2020 08:33:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:33:23: 32000000 INFO @ Tue, 14 Jul 2020 08:33:24: 28000000 INFO @ Tue, 14 Jul 2020 08:33:30: 33000000 INFO @ Tue, 14 Jul 2020 08:33:31: 29000000 INFO @ Tue, 14 Jul 2020 08:33:37: 34000000 INFO @ Tue, 14 Jul 2020 08:33:38: 30000000 INFO @ Tue, 14 Jul 2020 08:33:44: 35000000 INFO @ Tue, 14 Jul 2020 08:33:45: 31000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:33:51: 36000000 INFO @ Tue, 14 Jul 2020 08:33:52: 32000000 INFO @ Tue, 14 Jul 2020 08:33:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:33:56: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:33:56: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:33:56: #1 total tags in treatment: 17083939 INFO @ Tue, 14 Jul 2020 08:33:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:33:56: #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 08:33:56: #1 tags after filtering in treatment: 15173357 INFO @ Tue, 14 Jul 2020 08:33:56: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 08:33:56: #1 finished! INFO @ Tue, 14 Jul 2020 08:33:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:33:57: #2 number of paired peaks: 128 WARNING @ Tue, 14 Jul 2020 08:33:57: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 14 Jul 2020 08:33:57: start model_add_line... INFO @ Tue, 14 Jul 2020 08:33:57: start X-correlation... INFO @ Tue, 14 Jul 2020 08:33:57: end of X-cor INFO @ Tue, 14 Jul 2020 08:33:57: #2 finished! INFO @ Tue, 14 Jul 2020 08:33:57: #2 predicted fragment length is 160 bps INFO @ Tue, 14 Jul 2020 08:33:57: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 14 Jul 2020 08:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.10_model.r INFO @ Tue, 14 Jul 2020 08:33:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:33:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:33:59: 33000000 INFO @ Tue, 14 Jul 2020 08:34:06: 34000000 INFO @ Tue, 14 Jul 2020 08:34:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:34:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.05_summits.bed INFO @ Tue, 14 Jul 2020 08:34:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8414 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:34:12: 35000000 INFO @ Tue, 14 Jul 2020 08:34:19: 36000000 INFO @ Tue, 14 Jul 2020 08:34:23: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:34:23: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:34:23: #1 total tags in treatment: 17083939 INFO @ Tue, 14 Jul 2020 08:34:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:34:23: #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 08:34:23: #1 tags after filtering in treatment: 15173357 INFO @ Tue, 14 Jul 2020 08:34:23: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 08:34:23: #1 finished! INFO @ Tue, 14 Jul 2020 08:34:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:34:24: #2 number of paired peaks: 128 WARNING @ Tue, 14 Jul 2020 08:34:24: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 14 Jul 2020 08:34:24: start model_add_line... INFO @ Tue, 14 Jul 2020 08:34:24: start X-correlation... INFO @ Tue, 14 Jul 2020 08:34:24: end of X-cor INFO @ Tue, 14 Jul 2020 08:34:24: #2 finished! INFO @ Tue, 14 Jul 2020 08:34:24: #2 predicted fragment length is 160 bps INFO @ Tue, 14 Jul 2020 08:34:24: #2 alternative fragment length(s) may be 160 bps INFO @ Tue, 14 Jul 2020 08:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.20_model.r INFO @ Tue, 14 Jul 2020 08:34:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:34:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:34:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:34:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.10_summits.bed INFO @ Tue, 14 Jul 2020 08:34:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5018 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:34:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736463/SRX5736463.20_summits.bed INFO @ Tue, 14 Jul 2020 08:35:08: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (2184 records, 4 fields): 4 millis CompletedMACS2peakCalling