Job ID = 14172094 SRX = SRX7628905 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 37464621 spots for SRR10963267/SRR10963267.sra Written 37464621 spots for SRR10963267/SRR10963267.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172628 ("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: 00:28:58 37464621 reads; of these: 37464621 (100.00%) were paired; of these: 22740064 (60.70%) aligned concordantly 0 times 10554572 (28.17%) aligned concordantly exactly 1 time 4169985 (11.13%) aligned concordantly >1 times ---- 22740064 pairs aligned concordantly 0 times; of these: 52601 (0.23%) aligned discordantly 1 time ---- 22687463 pairs aligned 0 times concordantly or discordantly; of these: 45374926 mates make up the pairs; of these: 44589615 (98.27%) aligned 0 times 496326 (1.09%) aligned exactly 1 time 288985 (0.64%) aligned >1 times 40.49% overall alignment rate Time searching: 00:28:59 Overall time: 00:28:59 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 12 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] 831912 / 14766018 = 0.0563 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 14:46:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.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 14:46:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:46:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:46:49: 1000000 INFO @ Sat, 11 Dec 2021 14:46:53: 2000000 INFO @ Sat, 11 Dec 2021 14:46:58: 3000000 INFO @ Sat, 11 Dec 2021 14:47:03: 4000000 INFO @ Sat, 11 Dec 2021 14:47:08: 5000000 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 14:47:13: 6000000 INFO @ Sat, 11 Dec 2021 14:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.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 14:47:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:47:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:47:17: 7000000 INFO @ Sat, 11 Dec 2021 14:47:19: 1000000 INFO @ Sat, 11 Dec 2021 14:47:22: 8000000 INFO @ Sat, 11 Dec 2021 14:47:24: 2000000 INFO @ Sat, 11 Dec 2021 14:47:27: 9000000 INFO @ Sat, 11 Dec 2021 14:47:28: 3000000 INFO @ Sat, 11 Dec 2021 14:47:32: 10000000 INFO @ Sat, 11 Dec 2021 14:47:33: 4000000 INFO @ Sat, 11 Dec 2021 14:47:37: 11000000 INFO @ Sat, 11 Dec 2021 14:47:38: 5000000 INFO @ Sat, 11 Dec 2021 14:47:41: 12000000 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 14:47:43: 6000000 INFO @ Sat, 11 Dec 2021 14:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.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 14:47:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:47:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:47:46: 13000000 INFO @ Sat, 11 Dec 2021 14:47:48: 7000000 INFO @ Sat, 11 Dec 2021 14:47:49: 1000000 INFO @ Sat, 11 Dec 2021 14:47:51: 14000000 INFO @ Sat, 11 Dec 2021 14:47:53: 8000000 INFO @ Sat, 11 Dec 2021 14:47:54: 2000000 INFO @ Sat, 11 Dec 2021 14:47:56: 15000000 INFO @ Sat, 11 Dec 2021 14:47:58: 9000000 INFO @ Sat, 11 Dec 2021 14:47:59: 3000000 INFO @ Sat, 11 Dec 2021 14:48:01: 16000000 INFO @ Sat, 11 Dec 2021 14:48:03: 10000000 INFO @ Sat, 11 Dec 2021 14:48:04: 4000000 INFO @ Sat, 11 Dec 2021 14:48:07: 17000000 INFO @ Sat, 11 Dec 2021 14:48:08: 11000000 INFO @ Sat, 11 Dec 2021 14:48:09: 5000000 INFO @ Sat, 11 Dec 2021 14:48:12: 18000000 INFO @ Sat, 11 Dec 2021 14:48:13: 12000000 INFO @ Sat, 11 Dec 2021 14:48:14: 6000000 INFO @ Sat, 11 Dec 2021 14:48:17: 19000000 INFO @ Sat, 11 Dec 2021 14:48:18: 13000000 INFO @ Sat, 11 Dec 2021 14:48:19: 7000000 INFO @ Sat, 11 Dec 2021 14:48:22: 20000000 INFO @ Sat, 11 Dec 2021 14:48:23: 14000000 INFO @ Sat, 11 Dec 2021 14:48:24: 8000000 INFO @ Sat, 11 Dec 2021 14:48:27: 21000000 INFO @ Sat, 11 Dec 2021 14:48:28: 15000000 INFO @ Sat, 11 Dec 2021 14:48:29: 9000000 INFO @ Sat, 11 Dec 2021 14:48:32: 22000000 INFO @ Sat, 11 Dec 2021 14:48:33: 16000000 INFO @ Sat, 11 Dec 2021 14:48:34: 10000000 INFO @ Sat, 11 Dec 2021 14:48:37: 23000000 INFO @ Sat, 11 Dec 2021 14:48:38: 17000000 INFO @ Sat, 11 Dec 2021 14:48:39: 11000000 INFO @ Sat, 11 Dec 2021 14:48:42: 24000000 INFO @ Sat, 11 Dec 2021 14:48:43: 18000000 INFO @ Sat, 11 Dec 2021 14:48:45: 12000000 INFO @ Sat, 11 Dec 2021 14:48:47: 25000000 INFO @ Sat, 11 Dec 2021 14:48:48: 19000000 INFO @ Sat, 11 Dec 2021 14:48:50: 13000000 INFO @ Sat, 11 Dec 2021 14:48:52: 26000000 INFO @ Sat, 11 Dec 2021 14:48:53: 20000000 INFO @ Sat, 11 Dec 2021 14:48:55: 14000000 INFO @ Sat, 11 Dec 2021 14:48:57: 27000000 INFO @ Sat, 11 Dec 2021 14:48:58: 21000000 INFO @ Sat, 11 Dec 2021 14:49:00: 15000000 INFO @ Sat, 11 Dec 2021 14:49:02: 28000000 INFO @ Sat, 11 Dec 2021 14:49:03: 22000000 INFO @ Sat, 11 Dec 2021 14:49:05: 16000000 INFO @ Sat, 11 Dec 2021 14:49:05: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:49:05: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:49:05: #1 total tags in treatment: 13894609 INFO @ Sat, 11 Dec 2021 14:49:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:49:05: #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 14:49:06: #1 tags after filtering in treatment: 13008458 INFO @ Sat, 11 Dec 2021 14:49:06: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:49:06: #1 finished! INFO @ Sat, 11 Dec 2021 14:49:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:49:07: #2 number of paired peaks: 949 WARNING @ Sat, 11 Dec 2021 14:49:07: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Sat, 11 Dec 2021 14:49:07: start model_add_line... INFO @ Sat, 11 Dec 2021 14:49:07: start X-correlation... INFO @ Sat, 11 Dec 2021 14:49:07: end of X-cor INFO @ Sat, 11 Dec 2021 14:49:07: #2 finished! INFO @ Sat, 11 Dec 2021 14:49:07: #2 predicted fragment length is 122 bps INFO @ Sat, 11 Dec 2021 14:49:07: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 11 Dec 2021 14:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.05_model.r INFO @ Sat, 11 Dec 2021 14:49:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:49:08: 23000000 INFO @ Sat, 11 Dec 2021 14:49:10: 17000000 INFO @ Sat, 11 Dec 2021 14:49:13: 24000000 INFO @ Sat, 11 Dec 2021 14:49:15: 18000000 INFO @ Sat, 11 Dec 2021 14:49:18: 25000000 INFO @ Sat, 11 Dec 2021 14:49:20: 19000000 INFO @ Sat, 11 Dec 2021 14:49:23: 26000000 INFO @ Sat, 11 Dec 2021 14:49:25: 20000000 INFO @ Sat, 11 Dec 2021 14:49:28: 27000000 INFO @ Sat, 11 Dec 2021 14:49:30: 21000000 INFO @ Sat, 11 Dec 2021 14:49:32: 28000000 INFO @ Sat, 11 Dec 2021 14:49:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:49:35: 22000000 INFO @ Sat, 11 Dec 2021 14:49:36: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:49:36: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:49:36: #1 total tags in treatment: 13894609 INFO @ Sat, 11 Dec 2021 14:49:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:49:36: #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 14:49:36: #1 tags after filtering in treatment: 13008458 INFO @ Sat, 11 Dec 2021 14:49:36: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:49:36: #1 finished! INFO @ Sat, 11 Dec 2021 14:49:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:49:37: #2 number of paired peaks: 949 WARNING @ Sat, 11 Dec 2021 14:49:37: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Sat, 11 Dec 2021 14:49:37: start model_add_line... INFO @ Sat, 11 Dec 2021 14:49:37: start X-correlation... INFO @ Sat, 11 Dec 2021 14:49:37: end of X-cor INFO @ Sat, 11 Dec 2021 14:49:37: #2 finished! INFO @ Sat, 11 Dec 2021 14:49:37: #2 predicted fragment length is 122 bps INFO @ Sat, 11 Dec 2021 14:49:37: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 11 Dec 2021 14:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.10_model.r INFO @ Sat, 11 Dec 2021 14:49:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:49:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:49:40: 23000000 INFO @ Sat, 11 Dec 2021 14:49:44: 24000000 INFO @ Sat, 11 Dec 2021 14:49:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:49:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:49:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.05_summits.bed INFO @ Sat, 11 Dec 2021 14:49:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2768 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:49:49: 25000000 INFO @ Sat, 11 Dec 2021 14:49:54: 26000000 INFO @ Sat, 11 Dec 2021 14:49:59: 27000000 INFO @ Sat, 11 Dec 2021 14:50:04: 28000000 INFO @ Sat, 11 Dec 2021 14:50:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:50:07: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 14:50:07: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 14:50:07: #1 total tags in treatment: 13894609 INFO @ Sat, 11 Dec 2021 14:50:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:50:07: #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 14:50:08: #1 tags after filtering in treatment: 13008458 INFO @ Sat, 11 Dec 2021 14:50:08: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:50:08: #1 finished! INFO @ Sat, 11 Dec 2021 14:50:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:50:09: #2 number of paired peaks: 949 WARNING @ Sat, 11 Dec 2021 14:50:09: Fewer paired peaks (949) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 949 pairs to build model! INFO @ Sat, 11 Dec 2021 14:50:09: start model_add_line... INFO @ Sat, 11 Dec 2021 14:50:09: start X-correlation... INFO @ Sat, 11 Dec 2021 14:50:09: end of X-cor INFO @ Sat, 11 Dec 2021 14:50:09: #2 finished! INFO @ Sat, 11 Dec 2021 14:50:09: #2 predicted fragment length is 122 bps INFO @ Sat, 11 Dec 2021 14:50:09: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 11 Dec 2021 14:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.20_model.r INFO @ Sat, 11 Dec 2021 14:50:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:50:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:50:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:50:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.10_summits.bed INFO @ Sat, 11 Dec 2021 14:50:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1601 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:50:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:50:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628905/SRX7628905.20_summits.bed INFO @ Sat, 11 Dec 2021 14:50:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (757 records, 4 fields): 15 millis CompletedMACS2peakCalling