Job ID = 14170668 SRX = SRX9434475 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19922726 spots for SRR12982873/SRR12982873.sra Written 19922726 spots for SRR12982873/SRR12982873.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171240 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:41:49 19922726 reads; of these: 19922726 (100.00%) were paired; of these: 1277520 (6.41%) aligned concordantly 0 times 13405527 (67.29%) aligned concordantly exactly 1 time 5239679 (26.30%) aligned concordantly >1 times ---- 1277520 pairs aligned concordantly 0 times; of these: 81321 (6.37%) aligned discordantly 1 time ---- 1196199 pairs aligned 0 times concordantly or discordantly; of these: 2392398 mates make up the pairs; of these: 1338693 (55.96%) aligned 0 times 444767 (18.59%) aligned exactly 1 time 608938 (25.45%) aligned >1 times 96.64% overall alignment rate Time searching: 00:41:50 Overall time: 00:41:50 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] 1607401 / 18697404 = 0.0860 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 08:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.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 08:47:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:47:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:47:18: 1000000 INFO @ Sat, 11 Dec 2021 08:47:23: 2000000 INFO @ Sat, 11 Dec 2021 08:47:28: 3000000 INFO @ Sat, 11 Dec 2021 08:47:32: 4000000 INFO @ Sat, 11 Dec 2021 08:47:37: 5000000 INFO @ Sat, 11 Dec 2021 08:47:42: 6000000 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 08:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.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 08:47:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:47:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:47:46: 7000000 INFO @ Sat, 11 Dec 2021 08:47:49: 1000000 INFO @ Sat, 11 Dec 2021 08:47:51: 8000000 INFO @ Sat, 11 Dec 2021 08:47:54: 2000000 INFO @ Sat, 11 Dec 2021 08:47:56: 9000000 INFO @ Sat, 11 Dec 2021 08:47:59: 3000000 INFO @ Sat, 11 Dec 2021 08:48:01: 10000000 INFO @ Sat, 11 Dec 2021 08:48:04: 4000000 INFO @ Sat, 11 Dec 2021 08:48:06: 11000000 INFO @ Sat, 11 Dec 2021 08:48:09: 5000000 INFO @ Sat, 11 Dec 2021 08:48:11: 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 08:48:13: 6000000 INFO @ Sat, 11 Dec 2021 08:48:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.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 08:48:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:48:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:48:16: 13000000 INFO @ Sat, 11 Dec 2021 08:48:18: 7000000 INFO @ Sat, 11 Dec 2021 08:48:19: 1000000 INFO @ Sat, 11 Dec 2021 08:48:21: 14000000 INFO @ Sat, 11 Dec 2021 08:48:23: 8000000 INFO @ Sat, 11 Dec 2021 08:48:24: 2000000 INFO @ Sat, 11 Dec 2021 08:48:26: 15000000 INFO @ Sat, 11 Dec 2021 08:48:28: 9000000 INFO @ Sat, 11 Dec 2021 08:48:29: 3000000 INFO @ Sat, 11 Dec 2021 08:48:31: 16000000 INFO @ Sat, 11 Dec 2021 08:48:33: 10000000 INFO @ Sat, 11 Dec 2021 08:48:34: 4000000 INFO @ Sat, 11 Dec 2021 08:48:36: 17000000 INFO @ Sat, 11 Dec 2021 08:48:38: 11000000 INFO @ Sat, 11 Dec 2021 08:48:39: 5000000 INFO @ Sat, 11 Dec 2021 08:48:41: 18000000 INFO @ Sat, 11 Dec 2021 08:48:43: 12000000 INFO @ Sat, 11 Dec 2021 08:48:44: 6000000 INFO @ Sat, 11 Dec 2021 08:48:46: 19000000 INFO @ Sat, 11 Dec 2021 08:48:48: 13000000 INFO @ Sat, 11 Dec 2021 08:48:48: 7000000 INFO @ Sat, 11 Dec 2021 08:48:51: 20000000 INFO @ Sat, 11 Dec 2021 08:48:53: 14000000 INFO @ Sat, 11 Dec 2021 08:48:53: 8000000 INFO @ Sat, 11 Dec 2021 08:48:55: 21000000 INFO @ Sat, 11 Dec 2021 08:48:58: 15000000 INFO @ Sat, 11 Dec 2021 08:48:58: 9000000 INFO @ Sat, 11 Dec 2021 08:49:00: 22000000 INFO @ Sat, 11 Dec 2021 08:49:03: 16000000 INFO @ Sat, 11 Dec 2021 08:49:03: 10000000 INFO @ Sat, 11 Dec 2021 08:49:05: 23000000 INFO @ Sat, 11 Dec 2021 08:49:08: 17000000 INFO @ Sat, 11 Dec 2021 08:49:08: 11000000 INFO @ Sat, 11 Dec 2021 08:49:11: 24000000 INFO @ Sat, 11 Dec 2021 08:49:13: 18000000 INFO @ Sat, 11 Dec 2021 08:49:13: 12000000 INFO @ Sat, 11 Dec 2021 08:49:16: 25000000 INFO @ Sat, 11 Dec 2021 08:49:18: 19000000 INFO @ Sat, 11 Dec 2021 08:49:18: 13000000 INFO @ Sat, 11 Dec 2021 08:49:21: 26000000 INFO @ Sat, 11 Dec 2021 08:49:23: 20000000 INFO @ Sat, 11 Dec 2021 08:49:23: 14000000 INFO @ Sat, 11 Dec 2021 08:49:26: 27000000 INFO @ Sat, 11 Dec 2021 08:49:28: 21000000 INFO @ Sat, 11 Dec 2021 08:49:28: 15000000 INFO @ Sat, 11 Dec 2021 08:49:31: 28000000 INFO @ Sat, 11 Dec 2021 08:49:33: 22000000 INFO @ Sat, 11 Dec 2021 08:49:33: 16000000 INFO @ Sat, 11 Dec 2021 08:49:36: 29000000 INFO @ Sat, 11 Dec 2021 08:49:38: 23000000 INFO @ Sat, 11 Dec 2021 08:49:38: 17000000 INFO @ Sat, 11 Dec 2021 08:49:41: 30000000 INFO @ Sat, 11 Dec 2021 08:49:43: 24000000 INFO @ Sat, 11 Dec 2021 08:49:43: 18000000 INFO @ Sat, 11 Dec 2021 08:49:46: 31000000 INFO @ Sat, 11 Dec 2021 08:49:48: 25000000 INFO @ Sat, 11 Dec 2021 08:49:48: 19000000 INFO @ Sat, 11 Dec 2021 08:49:51: 32000000 INFO @ Sat, 11 Dec 2021 08:49:53: 20000000 INFO @ Sat, 11 Dec 2021 08:49:53: 26000000 INFO @ Sat, 11 Dec 2021 08:49:56: 33000000 INFO @ Sat, 11 Dec 2021 08:49:58: 21000000 INFO @ Sat, 11 Dec 2021 08:49:58: 27000000 INFO @ Sat, 11 Dec 2021 08:50:01: 34000000 INFO @ Sat, 11 Dec 2021 08:50:02: 22000000 INFO @ Sat, 11 Dec 2021 08:50:03: 28000000 INFO @ Sat, 11 Dec 2021 08:50:05: 35000000 INFO @ Sat, 11 Dec 2021 08:50:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:50:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:50:07: #1 total tags in treatment: 17042793 INFO @ Sat, 11 Dec 2021 08:50:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:50:07: #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 08:50:07: #1 tags after filtering in treatment: 16073299 INFO @ Sat, 11 Dec 2021 08:50:07: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:50:07: #1 finished! INFO @ Sat, 11 Dec 2021 08:50:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:50:07: 23000000 INFO @ Sat, 11 Dec 2021 08:50:08: 29000000 INFO @ Sat, 11 Dec 2021 08:50:08: #2 number of paired peaks: 451 WARNING @ Sat, 11 Dec 2021 08:50:08: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 11 Dec 2021 08:50:08: start model_add_line... INFO @ Sat, 11 Dec 2021 08:50:09: start X-correlation... INFO @ Sat, 11 Dec 2021 08:50:09: end of X-cor INFO @ Sat, 11 Dec 2021 08:50:09: #2 finished! INFO @ Sat, 11 Dec 2021 08:50:09: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Dec 2021 08:50:09: #2 alternative fragment length(s) may be 159,172 bps INFO @ Sat, 11 Dec 2021 08:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.05_model.r INFO @ Sat, 11 Dec 2021 08:50:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:50:12: 24000000 INFO @ Sat, 11 Dec 2021 08:50:12: 30000000 INFO @ Sat, 11 Dec 2021 08:50:17: 25000000 INFO @ Sat, 11 Dec 2021 08:50:17: 31000000 INFO @ Sat, 11 Dec 2021 08:50:22: 26000000 INFO @ Sat, 11 Dec 2021 08:50:22: 32000000 INFO @ Sat, 11 Dec 2021 08:50:27: 27000000 INFO @ Sat, 11 Dec 2021 08:50:27: 33000000 INFO @ Sat, 11 Dec 2021 08:50:32: 34000000 INFO @ Sat, 11 Dec 2021 08:50:32: 28000000 INFO @ Sat, 11 Dec 2021 08:50:37: 35000000 INFO @ Sat, 11 Dec 2021 08:50:37: 29000000 INFO @ Sat, 11 Dec 2021 08:50:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:50:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:50:38: #1 total tags in treatment: 17042793 INFO @ Sat, 11 Dec 2021 08:50:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:50:38: #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 08:50:39: #1 tags after filtering in treatment: 16073299 INFO @ Sat, 11 Dec 2021 08:50:39: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:50:39: #1 finished! INFO @ Sat, 11 Dec 2021 08:50:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:50:40: #2 number of paired peaks: 451 WARNING @ Sat, 11 Dec 2021 08:50:40: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 11 Dec 2021 08:50:40: start model_add_line... INFO @ Sat, 11 Dec 2021 08:50:40: start X-correlation... INFO @ Sat, 11 Dec 2021 08:50:40: end of X-cor INFO @ Sat, 11 Dec 2021 08:50:40: #2 finished! INFO @ Sat, 11 Dec 2021 08:50:40: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Dec 2021 08:50:40: #2 alternative fragment length(s) may be 159,172 bps INFO @ Sat, 11 Dec 2021 08:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.10_model.r INFO @ Sat, 11 Dec 2021 08:50:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:50:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:50:42: 30000000 INFO @ Sat, 11 Dec 2021 08:50:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:50:47: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:50:51: 32000000 INFO @ Sat, 11 Dec 2021 08:50:56: 33000000 INFO @ Sat, 11 Dec 2021 08:51:01: 34000000 INFO @ Sat, 11 Dec 2021 08:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.05_summits.bed INFO @ Sat, 11 Dec 2021 08:51:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2484 records, 4 fields): 112 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:51:05: 35000000 INFO @ Sat, 11 Dec 2021 08:51:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:51:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:51:07: #1 total tags in treatment: 17042793 INFO @ Sat, 11 Dec 2021 08:51:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:51:07: #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 08:51:07: #1 tags after filtering in treatment: 16073299 INFO @ Sat, 11 Dec 2021 08:51:07: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:51:07: #1 finished! INFO @ Sat, 11 Dec 2021 08:51:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:51:08: #2 number of paired peaks: 451 WARNING @ Sat, 11 Dec 2021 08:51:08: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sat, 11 Dec 2021 08:51:08: start model_add_line... INFO @ Sat, 11 Dec 2021 08:51:08: start X-correlation... INFO @ Sat, 11 Dec 2021 08:51:08: end of X-cor INFO @ Sat, 11 Dec 2021 08:51:08: #2 finished! INFO @ Sat, 11 Dec 2021 08:51:08: #2 predicted fragment length is 159 bps INFO @ Sat, 11 Dec 2021 08:51:08: #2 alternative fragment length(s) may be 159,172 bps INFO @ Sat, 11 Dec 2021 08:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.20_model.r INFO @ Sat, 11 Dec 2021 08:51:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:51:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.10_summits.bed INFO @ Sat, 11 Dec 2021 08:51:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1454 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:51:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434475/SRX9434475.20_summits.bed INFO @ Sat, 11 Dec 2021 08:52:01: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (742 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。