Job ID = 14171402 SRX = SRX9711627 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18487353 spots for SRR13282242/SRR13282242.sra Written 18487353 spots for SRR13282242/SRR13282242.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172104 ("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: 00:55:11 18487353 reads; of these: 18487353 (100.00%) were paired; of these: 2125696 (11.50%) aligned concordantly 0 times 12581098 (68.05%) aligned concordantly exactly 1 time 3780559 (20.45%) aligned concordantly >1 times ---- 2125696 pairs aligned concordantly 0 times; of these: 944719 (44.44%) aligned discordantly 1 time ---- 1180977 pairs aligned 0 times concordantly or discordantly; of these: 2361954 mates make up the pairs; of these: 1304160 (55.22%) aligned 0 times 399075 (16.90%) aligned exactly 1 time 658719 (27.89%) aligned >1 times 96.47% overall alignment rate Time searching: 00:55:11 Overall time: 00:55:11 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] 712062 / 17249125 = 0.0413 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 12:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.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 12:43:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:43:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:43:39: 1000000 INFO @ Sat, 11 Dec 2021 12:43:46: 2000000 INFO @ Sat, 11 Dec 2021 12:43:53: 3000000 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 12:43:59: 4000000 INFO @ Sat, 11 Dec 2021 12:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.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 12:44:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:07: 5000000 INFO @ Sat, 11 Dec 2021 12:44:10: 1000000 INFO @ Sat, 11 Dec 2021 12:44:14: 6000000 INFO @ Sat, 11 Dec 2021 12:44:18: 2000000 INFO @ Sat, 11 Dec 2021 12:44:22: 7000000 INFO @ Sat, 11 Dec 2021 12:44:26: 3000000 INFO @ Sat, 11 Dec 2021 12:44:29: 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 12:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.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 12:44:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:34: 4000000 INFO @ Sat, 11 Dec 2021 12:44:37: 9000000 INFO @ Sat, 11 Dec 2021 12:44:40: 1000000 INFO @ Sat, 11 Dec 2021 12:44:42: 5000000 INFO @ Sat, 11 Dec 2021 12:44:46: 10000000 INFO @ Sat, 11 Dec 2021 12:44:48: 2000000 INFO @ Sat, 11 Dec 2021 12:44:51: 6000000 INFO @ Sat, 11 Dec 2021 12:44:54: 11000000 INFO @ Sat, 11 Dec 2021 12:44:57: 3000000 INFO @ Sat, 11 Dec 2021 12:44:59: 7000000 INFO @ Sat, 11 Dec 2021 12:45:02: 12000000 INFO @ Sat, 11 Dec 2021 12:45:05: 4000000 INFO @ Sat, 11 Dec 2021 12:45:07: 8000000 INFO @ Sat, 11 Dec 2021 12:45:10: 13000000 INFO @ Sat, 11 Dec 2021 12:45:14: 5000000 INFO @ Sat, 11 Dec 2021 12:45:16: 9000000 INFO @ Sat, 11 Dec 2021 12:45:19: 14000000 INFO @ Sat, 11 Dec 2021 12:45:23: 6000000 INFO @ Sat, 11 Dec 2021 12:45:24: 10000000 INFO @ Sat, 11 Dec 2021 12:45:27: 15000000 INFO @ Sat, 11 Dec 2021 12:45:31: 7000000 INFO @ Sat, 11 Dec 2021 12:45:32: 11000000 INFO @ Sat, 11 Dec 2021 12:45:35: 16000000 INFO @ Sat, 11 Dec 2021 12:45:40: 8000000 INFO @ Sat, 11 Dec 2021 12:45:41: 12000000 INFO @ Sat, 11 Dec 2021 12:45:44: 17000000 INFO @ Sat, 11 Dec 2021 12:45:49: 9000000 INFO @ Sat, 11 Dec 2021 12:45:49: 13000000 INFO @ Sat, 11 Dec 2021 12:45:52: 18000000 INFO @ Sat, 11 Dec 2021 12:45:58: 14000000 INFO @ Sat, 11 Dec 2021 12:45:58: 10000000 INFO @ Sat, 11 Dec 2021 12:46:00: 19000000 INFO @ Sat, 11 Dec 2021 12:46:06: 15000000 INFO @ Sat, 11 Dec 2021 12:46:06: 11000000 INFO @ Sat, 11 Dec 2021 12:46:09: 20000000 INFO @ Sat, 11 Dec 2021 12:46:14: 16000000 INFO @ Sat, 11 Dec 2021 12:46:14: 12000000 INFO @ Sat, 11 Dec 2021 12:46:17: 21000000 INFO @ Sat, 11 Dec 2021 12:46:22: 17000000 INFO @ Sat, 11 Dec 2021 12:46:23: 13000000 INFO @ Sat, 11 Dec 2021 12:46:26: 22000000 INFO @ Sat, 11 Dec 2021 12:46:31: 18000000 INFO @ Sat, 11 Dec 2021 12:46:31: 14000000 INFO @ Sat, 11 Dec 2021 12:46:34: 23000000 INFO @ Sat, 11 Dec 2021 12:46:39: 19000000 INFO @ Sat, 11 Dec 2021 12:46:39: 15000000 INFO @ Sat, 11 Dec 2021 12:46:42: 24000000 INFO @ Sat, 11 Dec 2021 12:46:47: 20000000 INFO @ Sat, 11 Dec 2021 12:46:48: 16000000 INFO @ Sat, 11 Dec 2021 12:46:51: 25000000 INFO @ Sat, 11 Dec 2021 12:46:56: 21000000 INFO @ Sat, 11 Dec 2021 12:46:56: 17000000 INFO @ Sat, 11 Dec 2021 12:46:59: 26000000 INFO @ Sat, 11 Dec 2021 12:47:04: 22000000 INFO @ Sat, 11 Dec 2021 12:47:04: 18000000 INFO @ Sat, 11 Dec 2021 12:47:07: 27000000 INFO @ Sat, 11 Dec 2021 12:47:12: 23000000 INFO @ Sat, 11 Dec 2021 12:47:12: 19000000 INFO @ Sat, 11 Dec 2021 12:47:16: 28000000 INFO @ Sat, 11 Dec 2021 12:47:21: 24000000 INFO @ Sat, 11 Dec 2021 12:47:21: 20000000 INFO @ Sat, 11 Dec 2021 12:47:24: 29000000 INFO @ Sat, 11 Dec 2021 12:47:29: 25000000 INFO @ Sat, 11 Dec 2021 12:47:29: 21000000 INFO @ Sat, 11 Dec 2021 12:47:33: 30000000 INFO @ Sat, 11 Dec 2021 12:47:37: 26000000 INFO @ Sat, 11 Dec 2021 12:47:37: 22000000 INFO @ Sat, 11 Dec 2021 12:47:41: 31000000 INFO @ Sat, 11 Dec 2021 12:47:45: 23000000 INFO @ Sat, 11 Dec 2021 12:47:46: 27000000 INFO @ Sat, 11 Dec 2021 12:47:49: 32000000 INFO @ Sat, 11 Dec 2021 12:47:54: 24000000 INFO @ Sat, 11 Dec 2021 12:47:54: 28000000 INFO @ Sat, 11 Dec 2021 12:47:57: 33000000 INFO @ Sat, 11 Dec 2021 12:48:02: 25000000 INFO @ Sat, 11 Dec 2021 12:48:03: 29000000 INFO @ Sat, 11 Dec 2021 12:48:06: 34000000 INFO @ Sat, 11 Dec 2021 12:48:08: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:48:08: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:48:08: #1 total tags in treatment: 15688757 INFO @ Sat, 11 Dec 2021 12:48:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:48:08: #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 12:48:08: #1 tags after filtering in treatment: 14707363 INFO @ Sat, 11 Dec 2021 12:48:08: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:48:08: #1 finished! INFO @ Sat, 11 Dec 2021 12:48:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:48:09: #2 number of paired peaks: 446 WARNING @ Sat, 11 Dec 2021 12:48:09: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sat, 11 Dec 2021 12:48:09: start model_add_line... INFO @ Sat, 11 Dec 2021 12:48:09: start X-correlation... INFO @ Sat, 11 Dec 2021 12:48:09: end of X-cor INFO @ Sat, 11 Dec 2021 12:48:09: #2 finished! INFO @ Sat, 11 Dec 2021 12:48:09: #2 predicted fragment length is 230 bps INFO @ Sat, 11 Dec 2021 12:48:09: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 11 Dec 2021 12:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.05_model.r INFO @ Sat, 11 Dec 2021 12:48:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:48:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:48:11: 26000000 INFO @ Sat, 11 Dec 2021 12:48:11: 30000000 INFO @ Sat, 11 Dec 2021 12:48:18: 31000000 INFO @ Sat, 11 Dec 2021 12:48:18: 27000000 INFO @ Sat, 11 Dec 2021 12:48:26: 32000000 INFO @ Sat, 11 Dec 2021 12:48:26: 28000000 INFO @ Sat, 11 Dec 2021 12:48:34: 33000000 INFO @ Sat, 11 Dec 2021 12:48:34: 29000000 INFO @ Sat, 11 Dec 2021 12:48:41: 34000000 INFO @ Sat, 11 Dec 2021 12:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:48:42: 30000000 INFO @ Sat, 11 Dec 2021 12:48:43: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:48:43: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:48:43: #1 total tags in treatment: 15688757 INFO @ Sat, 11 Dec 2021 12:48:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:48:43: #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 12:48:43: #1 tags after filtering in treatment: 14707363 INFO @ Sat, 11 Dec 2021 12:48:43: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:48:43: #1 finished! INFO @ Sat, 11 Dec 2021 12:48:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:48:45: #2 number of paired peaks: 446 WARNING @ Sat, 11 Dec 2021 12:48:45: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sat, 11 Dec 2021 12:48:45: start model_add_line... INFO @ Sat, 11 Dec 2021 12:48:45: start X-correlation... INFO @ Sat, 11 Dec 2021 12:48:45: end of X-cor INFO @ Sat, 11 Dec 2021 12:48:45: #2 finished! INFO @ Sat, 11 Dec 2021 12:48:45: #2 predicted fragment length is 230 bps INFO @ Sat, 11 Dec 2021 12:48:45: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 11 Dec 2021 12:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.10_model.r INFO @ Sat, 11 Dec 2021 12:48:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:48:49: 31000000 INFO @ Sat, 11 Dec 2021 12:48:56: 32000000 INFO @ Sat, 11 Dec 2021 12:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:49:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.05_summits.bed INFO @ Sat, 11 Dec 2021 12:49:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3400 records, 4 fields): 689 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:49:04: 33000000 INFO @ Sat, 11 Dec 2021 12:49:11: 34000000 INFO @ Sat, 11 Dec 2021 12:49:12: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:49:12: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:49:12: #1 total tags in treatment: 15688757 INFO @ Sat, 11 Dec 2021 12:49:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:49:12: #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 12:49:13: #1 tags after filtering in treatment: 14707363 INFO @ Sat, 11 Dec 2021 12:49:13: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:49:13: #1 finished! INFO @ Sat, 11 Dec 2021 12:49:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:49:14: #2 number of paired peaks: 446 WARNING @ Sat, 11 Dec 2021 12:49:14: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sat, 11 Dec 2021 12:49:14: start model_add_line... INFO @ Sat, 11 Dec 2021 12:49:14: start X-correlation... INFO @ Sat, 11 Dec 2021 12:49:14: end of X-cor INFO @ Sat, 11 Dec 2021 12:49:14: #2 finished! INFO @ Sat, 11 Dec 2021 12:49:14: #2 predicted fragment length is 230 bps INFO @ Sat, 11 Dec 2021 12:49:14: #2 alternative fragment length(s) may be 230 bps INFO @ Sat, 11 Dec 2021 12:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.20_model.r INFO @ Sat, 11 Dec 2021 12:49:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:49:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:49:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:49:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:49:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.10_summits.bed INFO @ Sat, 11 Dec 2021 12:49:35: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1600 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:49:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711627/SRX9711627.20_summits.bed INFO @ Sat, 11 Dec 2021 12:50:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (749 records, 4 fields): 3 millis CompletedMACS2peakCalling