Job ID = 14171971 SRX = SRX7889132 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20512432 spots for SRR11283122/SRR11283122.sra Written 20512432 spots for SRR11283122/SRR11283122.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172583 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:48:18 20512432 reads; of these: 20512432 (100.00%) were paired; of these: 5961293 (29.06%) aligned concordantly 0 times 11600077 (56.55%) aligned concordantly exactly 1 time 2951062 (14.39%) aligned concordantly >1 times ---- 5961293 pairs aligned concordantly 0 times; of these: 1208093 (20.27%) aligned discordantly 1 time ---- 4753200 pairs aligned 0 times concordantly or discordantly; of these: 9506400 mates make up the pairs; of these: 7489557 (78.78%) aligned 0 times 1221840 (12.85%) aligned exactly 1 time 795003 (8.36%) aligned >1 times 81.74% overall alignment rate Time searching: 00:48:19 Overall time: 00:48:19 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 28 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] 2650172 / 14395453 = 0.1841 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 14:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.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 14:43:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:43:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:43:38: 1000000 INFO @ Sat, 11 Dec 2021 14:43:44: 2000000 INFO @ Sat, 11 Dec 2021 14:43:50: 3000000 INFO @ Sat, 11 Dec 2021 14:43:56: 4000000 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 14:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.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 14:44:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:44:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:44:03: 5000000 INFO @ Sat, 11 Dec 2021 14:44:08: 1000000 INFO @ Sat, 11 Dec 2021 14:44:09: 6000000 INFO @ Sat, 11 Dec 2021 14:44:15: 2000000 INFO @ Sat, 11 Dec 2021 14:44:16: 7000000 INFO @ Sat, 11 Dec 2021 14:44:22: 3000000 INFO @ Sat, 11 Dec 2021 14:44:22: 8000000 INFO @ Sat, 11 Dec 2021 14:44:28: 4000000 INFO @ Sat, 11 Dec 2021 14:44:29: 9000000 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 14:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.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 14:44:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:44:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:44:35: 5000000 INFO @ Sat, 11 Dec 2021 14:44:35: 10000000 INFO @ Sat, 11 Dec 2021 14:44:38: 1000000 INFO @ Sat, 11 Dec 2021 14:44:42: 11000000 INFO @ Sat, 11 Dec 2021 14:44:42: 6000000 INFO @ Sat, 11 Dec 2021 14:44:45: 2000000 INFO @ Sat, 11 Dec 2021 14:44:48: 12000000 INFO @ Sat, 11 Dec 2021 14:44:48: 7000000 INFO @ Sat, 11 Dec 2021 14:44:51: 3000000 INFO @ Sat, 11 Dec 2021 14:44:55: 13000000 INFO @ Sat, 11 Dec 2021 14:44:55: 8000000 INFO @ Sat, 11 Dec 2021 14:44:58: 4000000 INFO @ Sat, 11 Dec 2021 14:45:01: 14000000 INFO @ Sat, 11 Dec 2021 14:45:02: 9000000 INFO @ Sat, 11 Dec 2021 14:45:04: 5000000 INFO @ Sat, 11 Dec 2021 14:45:08: 15000000 INFO @ Sat, 11 Dec 2021 14:45:08: 10000000 INFO @ Sat, 11 Dec 2021 14:45:11: 6000000 INFO @ Sat, 11 Dec 2021 14:45:14: 16000000 INFO @ Sat, 11 Dec 2021 14:45:15: 11000000 INFO @ Sat, 11 Dec 2021 14:45:17: 7000000 INFO @ Sat, 11 Dec 2021 14:45:20: 17000000 INFO @ Sat, 11 Dec 2021 14:45:22: 12000000 INFO @ Sat, 11 Dec 2021 14:45:24: 8000000 INFO @ Sat, 11 Dec 2021 14:45:27: 18000000 INFO @ Sat, 11 Dec 2021 14:45:28: 13000000 INFO @ Sat, 11 Dec 2021 14:45:30: 9000000 INFO @ Sat, 11 Dec 2021 14:45:33: 19000000 INFO @ Sat, 11 Dec 2021 14:45:35: 14000000 INFO @ Sat, 11 Dec 2021 14:45:37: 10000000 INFO @ Sat, 11 Dec 2021 14:45:40: 20000000 INFO @ Sat, 11 Dec 2021 14:45:41: 15000000 INFO @ Sat, 11 Dec 2021 14:45:43: 11000000 INFO @ Sat, 11 Dec 2021 14:45:46: 21000000 INFO @ Sat, 11 Dec 2021 14:45:48: 16000000 INFO @ Sat, 11 Dec 2021 14:45:50: 12000000 INFO @ Sat, 11 Dec 2021 14:45:53: 22000000 INFO @ Sat, 11 Dec 2021 14:45:55: 17000000 INFO @ Sat, 11 Dec 2021 14:45:56: 13000000 INFO @ Sat, 11 Dec 2021 14:45:59: 23000000 INFO @ Sat, 11 Dec 2021 14:46:01: 18000000 INFO @ Sat, 11 Dec 2021 14:46:03: 14000000 INFO @ Sat, 11 Dec 2021 14:46:06: 24000000 INFO @ Sat, 11 Dec 2021 14:46:08: 19000000 INFO @ Sat, 11 Dec 2021 14:46:09: 15000000 INFO @ Sat, 11 Dec 2021 14:46:12: 25000000 INFO @ Sat, 11 Dec 2021 14:46:14: 20000000 INFO @ Sat, 11 Dec 2021 14:46:16: 16000000 INFO @ Sat, 11 Dec 2021 14:46:18: 26000000 INFO @ Sat, 11 Dec 2021 14:46:21: 21000000 INFO @ Sat, 11 Dec 2021 14:46:22: 17000000 INFO @ Sat, 11 Dec 2021 14:46:25: 27000000 INFO @ Sat, 11 Dec 2021 14:46:27: 22000000 INFO @ Sat, 11 Dec 2021 14:46:28: 18000000 INFO @ Sat, 11 Dec 2021 14:46:31: 28000000 INFO @ Sat, 11 Dec 2021 14:46:33: #1 tag size is determined as 103 bps INFO @ Sat, 11 Dec 2021 14:46:33: #1 tag size = 103 INFO @ Sat, 11 Dec 2021 14:46:33: #1 total tags in treatment: 12056110 INFO @ Sat, 11 Dec 2021 14:46:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:46:33: #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 14:46:33: #1 tags after filtering in treatment: 11346754 INFO @ Sat, 11 Dec 2021 14:46:33: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:46:33: #1 finished! INFO @ Sat, 11 Dec 2021 14:46:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:46:34: #2 number of paired peaks: 519 WARNING @ Sat, 11 Dec 2021 14:46:34: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Sat, 11 Dec 2021 14:46:34: start model_add_line... INFO @ Sat, 11 Dec 2021 14:46:34: start X-correlation... INFO @ Sat, 11 Dec 2021 14:46:34: end of X-cor INFO @ Sat, 11 Dec 2021 14:46:34: #2 finished! INFO @ Sat, 11 Dec 2021 14:46:34: #2 predicted fragment length is 243 bps INFO @ Sat, 11 Dec 2021 14:46:34: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 11 Dec 2021 14:46:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.05_model.r INFO @ Sat, 11 Dec 2021 14:46:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:46:34: 23000000 INFO @ Sat, 11 Dec 2021 14:46:35: 19000000 INFO @ Sat, 11 Dec 2021 14:46:40: 24000000 INFO @ Sat, 11 Dec 2021 14:46:41: 20000000 INFO @ Sat, 11 Dec 2021 14:46:47: 25000000 INFO @ Sat, 11 Dec 2021 14:46:48: 21000000 INFO @ Sat, 11 Dec 2021 14:46:53: 26000000 INFO @ Sat, 11 Dec 2021 14:46:54: 22000000 INFO @ Sat, 11 Dec 2021 14:46:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:47:00: 27000000 INFO @ Sat, 11 Dec 2021 14:47:00: 23000000 INFO @ Sat, 11 Dec 2021 14:47:06: 28000000 INFO @ Sat, 11 Dec 2021 14:47:07: 24000000 INFO @ Sat, 11 Dec 2021 14:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.05_summits.bed INFO @ Sat, 11 Dec 2021 14:47:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5274 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:47:08: #1 tag size is determined as 103 bps INFO @ Sat, 11 Dec 2021 14:47:08: #1 tag size = 103 INFO @ Sat, 11 Dec 2021 14:47:08: #1 total tags in treatment: 12056110 INFO @ Sat, 11 Dec 2021 14:47:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:47:08: #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 14:47:08: #1 tags after filtering in treatment: 11346754 INFO @ Sat, 11 Dec 2021 14:47:08: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:47:08: #1 finished! INFO @ Sat, 11 Dec 2021 14:47:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:47:09: #2 number of paired peaks: 519 WARNING @ Sat, 11 Dec 2021 14:47:09: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Sat, 11 Dec 2021 14:47:09: start model_add_line... INFO @ Sat, 11 Dec 2021 14:47:09: start X-correlation... INFO @ Sat, 11 Dec 2021 14:47:09: end of X-cor INFO @ Sat, 11 Dec 2021 14:47:09: #2 finished! INFO @ Sat, 11 Dec 2021 14:47:09: #2 predicted fragment length is 243 bps INFO @ Sat, 11 Dec 2021 14:47:09: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 11 Dec 2021 14:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.10_model.r INFO @ Sat, 11 Dec 2021 14:47:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:47:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:47:13: 25000000 INFO @ Sat, 11 Dec 2021 14:47:19: 26000000 INFO @ Sat, 11 Dec 2021 14:47:26: 27000000 INFO @ Sat, 11 Dec 2021 14:47:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:47:32: 28000000 INFO @ Sat, 11 Dec 2021 14:47:34: #1 tag size is determined as 103 bps INFO @ Sat, 11 Dec 2021 14:47:34: #1 tag size = 103 INFO @ Sat, 11 Dec 2021 14:47:34: #1 total tags in treatment: 12056110 INFO @ Sat, 11 Dec 2021 14:47:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:47:34: #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 14:47:34: #1 tags after filtering in treatment: 11346754 INFO @ Sat, 11 Dec 2021 14:47:34: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 14:47:34: #1 finished! INFO @ Sat, 11 Dec 2021 14:47:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:47:35: #2 number of paired peaks: 519 WARNING @ Sat, 11 Dec 2021 14:47:35: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Sat, 11 Dec 2021 14:47:35: start model_add_line... INFO @ Sat, 11 Dec 2021 14:47:35: start X-correlation... INFO @ Sat, 11 Dec 2021 14:47:35: end of X-cor INFO @ Sat, 11 Dec 2021 14:47:35: #2 finished! INFO @ Sat, 11 Dec 2021 14:47:35: #2 predicted fragment length is 243 bps INFO @ Sat, 11 Dec 2021 14:47:35: #2 alternative fragment length(s) may be 243 bps INFO @ Sat, 11 Dec 2021 14:47:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.20_model.r INFO @ Sat, 11 Dec 2021 14:47:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.10_summits.bed INFO @ Sat, 11 Dec 2021 14:47:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2880 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:47:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889132/SRX7889132.20_summits.bed INFO @ Sat, 11 Dec 2021 14:48:08: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1457 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。