Job ID = 14172463 SRX = SRX7541442 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33225726 spots for SRR10871478/SRR10871478.sra Written 33225726 spots for SRR10871478/SRR10871478.sra fastq に変換しました。 bowtie でマッピング中... Your job 14173183 ("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: 01:21:15 33225726 reads; of these: 33225726 (100.00%) were paired; of these: 10529214 (31.69%) aligned concordantly 0 times 15415310 (46.40%) aligned concordantly exactly 1 time 7281202 (21.91%) aligned concordantly >1 times ---- 10529214 pairs aligned concordantly 0 times; of these: 324727 (3.08%) aligned discordantly 1 time ---- 10204487 pairs aligned 0 times concordantly or discordantly; of these: 20408974 mates make up the pairs; of these: 19283374 (94.48%) aligned 0 times 525103 (2.57%) aligned exactly 1 time 600497 (2.94%) aligned >1 times 70.98% overall alignment rate Time searching: 01:21:15 Overall time: 01:21:15 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] 5669507 / 22907120 = 0.2475 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 17:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.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 17:09:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:09:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:09:52: 1000000 INFO @ Sat, 11 Dec 2021 17:09:59: 2000000 INFO @ Sat, 11 Dec 2021 17:10:06: 3000000 INFO @ Sat, 11 Dec 2021 17:10:12: 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 17:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.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 17:10:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:10:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:10:20: 5000000 INFO @ Sat, 11 Dec 2021 17:10:23: 1000000 INFO @ Sat, 11 Dec 2021 17:10:28: 6000000 INFO @ Sat, 11 Dec 2021 17:10:31: 2000000 INFO @ Sat, 11 Dec 2021 17:10:36: 7000000 INFO @ Sat, 11 Dec 2021 17:10:39: 3000000 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 17:10:44: 8000000 INFO @ Sat, 11 Dec 2021 17:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.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 17:10:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:10:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:10:48: 4000000 INFO @ Sat, 11 Dec 2021 17:10:54: 9000000 INFO @ Sat, 11 Dec 2021 17:10:55: 1000000 INFO @ Sat, 11 Dec 2021 17:10:57: 5000000 INFO @ Sat, 11 Dec 2021 17:11:03: 10000000 INFO @ Sat, 11 Dec 2021 17:11:05: 2000000 INFO @ Sat, 11 Dec 2021 17:11:07: 6000000 INFO @ Sat, 11 Dec 2021 17:11:12: 11000000 INFO @ Sat, 11 Dec 2021 17:11:16: 3000000 INFO @ Sat, 11 Dec 2021 17:11:16: 7000000 INFO @ Sat, 11 Dec 2021 17:11:21: 12000000 INFO @ Sat, 11 Dec 2021 17:11:25: 8000000 INFO @ Sat, 11 Dec 2021 17:11:26: 4000000 INFO @ Sat, 11 Dec 2021 17:11:31: 13000000 INFO @ Sat, 11 Dec 2021 17:11:34: 9000000 INFO @ Sat, 11 Dec 2021 17:11:36: 5000000 INFO @ Sat, 11 Dec 2021 17:11:40: 14000000 INFO @ Sat, 11 Dec 2021 17:11:43: 10000000 INFO @ Sat, 11 Dec 2021 17:11:46: 6000000 INFO @ Sat, 11 Dec 2021 17:11:50: 15000000 INFO @ Sat, 11 Dec 2021 17:11:53: 11000000 INFO @ Sat, 11 Dec 2021 17:11:56: 7000000 INFO @ Sat, 11 Dec 2021 17:11:59: 16000000 INFO @ Sat, 11 Dec 2021 17:12:02: 12000000 INFO @ Sat, 11 Dec 2021 17:12:06: 8000000 INFO @ Sat, 11 Dec 2021 17:12:08: 17000000 INFO @ Sat, 11 Dec 2021 17:12:11: 13000000 INFO @ Sat, 11 Dec 2021 17:12:16: 9000000 INFO @ Sat, 11 Dec 2021 17:12:18: 18000000 INFO @ Sat, 11 Dec 2021 17:12:21: 14000000 INFO @ Sat, 11 Dec 2021 17:12:26: 10000000 INFO @ Sat, 11 Dec 2021 17:12:27: 19000000 INFO @ Sat, 11 Dec 2021 17:12:30: 15000000 INFO @ Sat, 11 Dec 2021 17:12:36: 20000000 INFO @ Sat, 11 Dec 2021 17:12:36: 11000000 INFO @ Sat, 11 Dec 2021 17:12:39: 16000000 INFO @ Sat, 11 Dec 2021 17:12:46: 21000000 INFO @ Sat, 11 Dec 2021 17:12:47: 12000000 INFO @ Sat, 11 Dec 2021 17:12:49: 17000000 INFO @ Sat, 11 Dec 2021 17:12:55: 22000000 INFO @ Sat, 11 Dec 2021 17:12:57: 13000000 INFO @ Sat, 11 Dec 2021 17:12:58: 18000000 INFO @ Sat, 11 Dec 2021 17:13:04: 23000000 INFO @ Sat, 11 Dec 2021 17:13:07: 14000000 INFO @ Sat, 11 Dec 2021 17:13:08: 19000000 INFO @ Sat, 11 Dec 2021 17:13:14: 24000000 INFO @ Sat, 11 Dec 2021 17:13:17: 20000000 INFO @ Sat, 11 Dec 2021 17:13:17: 15000000 INFO @ Sat, 11 Dec 2021 17:13:23: 25000000 INFO @ Sat, 11 Dec 2021 17:13:26: 21000000 INFO @ Sat, 11 Dec 2021 17:13:27: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 17:13:33: 26000000 INFO @ Sat, 11 Dec 2021 17:13:35: 22000000 INFO @ Sat, 11 Dec 2021 17:13:38: 17000000 INFO @ Sat, 11 Dec 2021 17:13:42: 27000000 INFO @ Sat, 11 Dec 2021 17:13:45: 23000000 INFO @ Sat, 11 Dec 2021 17:13:48: 18000000 INFO @ Sat, 11 Dec 2021 17:13:51: 28000000 INFO @ Sat, 11 Dec 2021 17:13:54: 24000000 INFO @ Sat, 11 Dec 2021 17:13:58: 19000000 INFO @ Sat, 11 Dec 2021 17:14:01: 29000000 INFO @ Sat, 11 Dec 2021 17:14:03: 25000000 INFO @ Sat, 11 Dec 2021 17:14:08: 20000000 INFO @ Sat, 11 Dec 2021 17:14:11: 30000000 INFO @ Sat, 11 Dec 2021 17:14:13: 26000000 INFO @ Sat, 11 Dec 2021 17:14:18: 21000000 INFO @ Sat, 11 Dec 2021 17:14:20: 31000000 INFO @ Sat, 11 Dec 2021 17:14:22: 27000000 INFO @ Sat, 11 Dec 2021 17:14:28: 22000000 INFO @ Sat, 11 Dec 2021 17:14:30: 32000000 INFO @ Sat, 11 Dec 2021 17:14:31: 28000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 17:14:38: 23000000 INFO @ Sat, 11 Dec 2021 17:14:40: 33000000 INFO @ Sat, 11 Dec 2021 17:14:41: 29000000 INFO @ Sat, 11 Dec 2021 17:14:49: 24000000 INFO @ Sat, 11 Dec 2021 17:14:49: 34000000 INFO @ Sat, 11 Dec 2021 17:14:50: 30000000 INFO @ Sat, 11 Dec 2021 17:14:58: 35000000 INFO @ Sat, 11 Dec 2021 17:14:59: 25000000 INFO @ Sat, 11 Dec 2021 17:14:59: 31000000 INFO @ Sat, 11 Dec 2021 17:15:06: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 17:15:06: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 17:15:06: #1 total tags in treatment: 17065820 INFO @ Sat, 11 Dec 2021 17:15:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:15:06: #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 17:15:07: #1 tags after filtering in treatment: 14211920 INFO @ Sat, 11 Dec 2021 17:15:07: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 17:15:07: #1 finished! INFO @ Sat, 11 Dec 2021 17:15:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:15:07: #2 number of paired peaks: 158 WARNING @ Sat, 11 Dec 2021 17:15:07: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 11 Dec 2021 17:15:07: start model_add_line... INFO @ Sat, 11 Dec 2021 17:15:08: start X-correlation... INFO @ Sat, 11 Dec 2021 17:15:08: end of X-cor INFO @ Sat, 11 Dec 2021 17:15:08: #2 finished! INFO @ Sat, 11 Dec 2021 17:15:08: #2 predicted fragment length is 132 bps INFO @ Sat, 11 Dec 2021 17:15:08: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 11 Dec 2021 17:15:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.05_model.r WARNING @ Sat, 11 Dec 2021 17:15:08: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:15:08: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 11 Dec 2021 17:15:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:15:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:15:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:15:09: 32000000 INFO @ Sat, 11 Dec 2021 17:15:09: 26000000 INFO @ Sat, 11 Dec 2021 17:15:18: 33000000 INFO @ Sat, 11 Dec 2021 17:15:19: 27000000 INFO @ Sat, 11 Dec 2021 17:15:26: 34000000 INFO @ Sat, 11 Dec 2021 17:15:29: 28000000 INFO @ Sat, 11 Dec 2021 17:15:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:15:35: 35000000 INFO @ Sat, 11 Dec 2021 17:15:39: 29000000 INFO @ Sat, 11 Dec 2021 17:15:43: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 17:15:43: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 17:15:43: #1 total tags in treatment: 17065820 INFO @ Sat, 11 Dec 2021 17:15:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:15:43: #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 17:15:43: #1 tags after filtering in treatment: 14211920 INFO @ Sat, 11 Dec 2021 17:15:43: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 17:15:43: #1 finished! INFO @ Sat, 11 Dec 2021 17:15:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:15:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:15:44: #2 number of paired peaks: 158 WARNING @ Sat, 11 Dec 2021 17:15:44: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 11 Dec 2021 17:15:44: start model_add_line... INFO @ Sat, 11 Dec 2021 17:15:44: start X-correlation... INFO @ Sat, 11 Dec 2021 17:15:44: end of X-cor INFO @ Sat, 11 Dec 2021 17:15:44: #2 finished! INFO @ Sat, 11 Dec 2021 17:15:44: #2 predicted fragment length is 132 bps INFO @ Sat, 11 Dec 2021 17:15:44: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 11 Dec 2021 17:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.10_model.r WARNING @ Sat, 11 Dec 2021 17:15:44: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:15:44: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 11 Dec 2021 17:15:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:15:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.05_peaks.xls INFO @ Sat, 11 Dec 2021 17:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.05_summits.bed INFO @ Sat, 11 Dec 2021 17:15:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3538 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:15:49: 30000000 INFO @ Sat, 11 Dec 2021 17:15:57: 31000000 INFO @ Sat, 11 Dec 2021 17:16:06: 32000000 INFO @ Sat, 11 Dec 2021 17:16:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:16:14: 33000000 INFO @ Sat, 11 Dec 2021 17:16:22: 34000000 INFO @ Sat, 11 Dec 2021 17:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.10_peaks.xls INFO @ Sat, 11 Dec 2021 17:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.10_summits.bed INFO @ Sat, 11 Dec 2021 17:16:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1532 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:16:31: 35000000 INFO @ Sat, 11 Dec 2021 17:16:37: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 17:16:37: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 17:16:37: #1 total tags in treatment: 17065820 INFO @ Sat, 11 Dec 2021 17:16:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:16:37: #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 17:16:38: #1 tags after filtering in treatment: 14211920 INFO @ Sat, 11 Dec 2021 17:16:38: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 17:16:38: #1 finished! INFO @ Sat, 11 Dec 2021 17:16:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:16:39: #2 number of paired peaks: 158 WARNING @ Sat, 11 Dec 2021 17:16:39: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 11 Dec 2021 17:16:39: start model_add_line... INFO @ Sat, 11 Dec 2021 17:16:39: start X-correlation... INFO @ Sat, 11 Dec 2021 17:16:39: end of X-cor INFO @ Sat, 11 Dec 2021 17:16:39: #2 finished! INFO @ Sat, 11 Dec 2021 17:16:39: #2 predicted fragment length is 132 bps INFO @ Sat, 11 Dec 2021 17:16:39: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 11 Dec 2021 17:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.20_model.r WARNING @ Sat, 11 Dec 2021 17:16:39: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:16:39: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 11 Dec 2021 17:16:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:16:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:17:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.20_peaks.xls INFO @ Sat, 11 Dec 2021 17:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541442/SRX7541442.20_summits.bed INFO @ Sat, 11 Dec 2021 17:17:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 2 millis CompletedMACS2peakCalling