Job ID = 14171423 SRX = SRX9711630 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17574567 spots for SRR13282245/SRR13282245.sra Written 17574567 spots for SRR13282245/SRR13282245.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172011 ("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: 00:25:48 17574567 reads; of these: 17574567 (100.00%) were paired; of these: 4893154 (27.84%) aligned concordantly 0 times 10860092 (61.79%) aligned concordantly exactly 1 time 1821321 (10.36%) aligned concordantly >1 times ---- 4893154 pairs aligned concordantly 0 times; of these: 1765391 (36.08%) aligned discordantly 1 time ---- 3127763 pairs aligned 0 times concordantly or discordantly; of these: 6255526 mates make up the pairs; of these: 5229500 (83.60%) aligned 0 times 462720 (7.40%) aligned exactly 1 time 563306 (9.00%) aligned >1 times 85.12% overall alignment rate Time searching: 00:25:48 Overall time: 00:25:48 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] 265369 / 14324980 = 0.0185 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 12:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.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 12:12:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:12:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:12:09: 1000000 INFO @ Sat, 11 Dec 2021 12:12:15: 2000000 INFO @ Sat, 11 Dec 2021 12:12:22: 3000000 INFO @ Sat, 11 Dec 2021 12:12:28: 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 12:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.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 12:12:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:12:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:12:34: 5000000 INFO @ Sat, 11 Dec 2021 12:12:38: 1000000 INFO @ Sat, 11 Dec 2021 12:12:41: 6000000 INFO @ Sat, 11 Dec 2021 12:12:44: 2000000 INFO @ Sat, 11 Dec 2021 12:12:47: 7000000 INFO @ Sat, 11 Dec 2021 12:12:49: 3000000 INFO @ Sat, 11 Dec 2021 12:12:54: 8000000 INFO @ Sat, 11 Dec 2021 12:12:55: 4000000 INFO @ Sat, 11 Dec 2021 12:13:00: 5000000 INFO @ Sat, 11 Dec 2021 12:13:01: 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 12:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.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 12:13:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:13:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:13:06: 6000000 INFO @ Sat, 11 Dec 2021 12:13:07: 10000000 INFO @ Sat, 11 Dec 2021 12:13:08: 1000000 INFO @ Sat, 11 Dec 2021 12:13:11: 7000000 INFO @ Sat, 11 Dec 2021 12:13:14: 11000000 INFO @ Sat, 11 Dec 2021 12:13:14: 2000000 INFO @ Sat, 11 Dec 2021 12:13:17: 8000000 INFO @ Sat, 11 Dec 2021 12:13:19: 3000000 INFO @ Sat, 11 Dec 2021 12:13:20: 12000000 INFO @ Sat, 11 Dec 2021 12:13:22: 9000000 INFO @ Sat, 11 Dec 2021 12:13:25: 4000000 INFO @ Sat, 11 Dec 2021 12:13:27: 13000000 INFO @ Sat, 11 Dec 2021 12:13:28: 10000000 INFO @ Sat, 11 Dec 2021 12:13:30: 5000000 INFO @ Sat, 11 Dec 2021 12:13:33: 11000000 INFO @ Sat, 11 Dec 2021 12:13:33: 14000000 INFO @ Sat, 11 Dec 2021 12:13:36: 6000000 INFO @ Sat, 11 Dec 2021 12:13:39: 12000000 INFO @ Sat, 11 Dec 2021 12:13:40: 15000000 INFO @ Sat, 11 Dec 2021 12:13:41: 7000000 INFO @ Sat, 11 Dec 2021 12:13:44: 13000000 INFO @ Sat, 11 Dec 2021 12:13:46: 16000000 INFO @ Sat, 11 Dec 2021 12:13:47: 8000000 INFO @ Sat, 11 Dec 2021 12:13:50: 14000000 INFO @ Sat, 11 Dec 2021 12:13:52: 9000000 INFO @ Sat, 11 Dec 2021 12:13:53: 17000000 INFO @ Sat, 11 Dec 2021 12:13:55: 15000000 INFO @ Sat, 11 Dec 2021 12:13:58: 10000000 INFO @ Sat, 11 Dec 2021 12:13:59: 18000000 INFO @ Sat, 11 Dec 2021 12:14:00: 16000000 INFO @ Sat, 11 Dec 2021 12:14:03: 11000000 INFO @ Sat, 11 Dec 2021 12:14:06: 19000000 INFO @ Sat, 11 Dec 2021 12:14:06: 17000000 INFO @ Sat, 11 Dec 2021 12:14:08: 12000000 INFO @ Sat, 11 Dec 2021 12:14:11: 18000000 INFO @ Sat, 11 Dec 2021 12:14:12: 20000000 INFO @ Sat, 11 Dec 2021 12:14:14: 13000000 INFO @ Sat, 11 Dec 2021 12:14:17: 19000000 INFO @ Sat, 11 Dec 2021 12:14:18: 21000000 INFO @ Sat, 11 Dec 2021 12:14:19: 14000000 INFO @ Sat, 11 Dec 2021 12:14:22: 20000000 INFO @ Sat, 11 Dec 2021 12:14:25: 15000000 INFO @ Sat, 11 Dec 2021 12:14:25: 22000000 INFO @ Sat, 11 Dec 2021 12:14:27: 21000000 INFO @ Sat, 11 Dec 2021 12:14:30: 16000000 INFO @ Sat, 11 Dec 2021 12:14:31: 23000000 INFO @ Sat, 11 Dec 2021 12:14:33: 22000000 INFO @ Sat, 11 Dec 2021 12:14:35: 17000000 INFO @ Sat, 11 Dec 2021 12:14:38: 24000000 INFO @ Sat, 11 Dec 2021 12:14:38: 23000000 INFO @ Sat, 11 Dec 2021 12:14:41: 18000000 INFO @ Sat, 11 Dec 2021 12:14:44: 24000000 INFO @ Sat, 11 Dec 2021 12:14:44: 25000000 INFO @ Sat, 11 Dec 2021 12:14:46: 19000000 INFO @ Sat, 11 Dec 2021 12:14:49: 25000000 INFO @ Sat, 11 Dec 2021 12:14:50: 26000000 INFO @ Sat, 11 Dec 2021 12:14:52: 20000000 INFO @ Sat, 11 Dec 2021 12:14:55: 26000000 INFO @ Sat, 11 Dec 2021 12:14:57: 27000000 INFO @ Sat, 11 Dec 2021 12:14:57: 21000000 INFO @ Sat, 11 Dec 2021 12:15:00: 27000000 INFO @ Sat, 11 Dec 2021 12:15:02: 22000000 INFO @ Sat, 11 Dec 2021 12:15:03: 28000000 INFO @ Sat, 11 Dec 2021 12:15:06: 28000000 INFO @ Sat, 11 Dec 2021 12:15:08: 23000000 INFO @ Sat, 11 Dec 2021 12:15:09: 29000000 INFO @ Sat, 11 Dec 2021 12:15:11: 29000000 INFO @ Sat, 11 Dec 2021 12:15:12: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:15:12: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:15:12: #1 total tags in treatment: 12442886 INFO @ Sat, 11 Dec 2021 12:15:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:15:12: #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 12:15:12: #1 tags after filtering in treatment: 11589727 INFO @ Sat, 11 Dec 2021 12:15:12: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 12:15:12: #1 finished! INFO @ Sat, 11 Dec 2021 12:15:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:15:13: #2 number of paired peaks: 108 WARNING @ Sat, 11 Dec 2021 12:15:13: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 11 Dec 2021 12:15:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:15:13: start X-correlation... INFO @ Sat, 11 Dec 2021 12:15:13: end of X-cor INFO @ Sat, 11 Dec 2021 12:15:13: #2 finished! INFO @ Sat, 11 Dec 2021 12:15:13: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 12:15:13: #2 alternative fragment length(s) may be 4,154,168,580 bps INFO @ Sat, 11 Dec 2021 12:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.05_model.r WARNING @ Sat, 11 Dec 2021 12:15:13: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:15:13: #2 You may need to consider one of the other alternative d(s): 4,154,168,580 WARNING @ Sat, 11 Dec 2021 12:15:13: #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 12:15:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:15:13: 24000000 INFO @ Sat, 11 Dec 2021 12:15:13: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:15:13: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:15:13: #1 total tags in treatment: 12442886 INFO @ Sat, 11 Dec 2021 12:15:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:15:13: #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 12:15:14: #1 tags after filtering in treatment: 11589727 INFO @ Sat, 11 Dec 2021 12:15:14: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 12:15:14: #1 finished! INFO @ Sat, 11 Dec 2021 12:15:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:15:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:15:14: #2 number of paired peaks: 108 WARNING @ Sat, 11 Dec 2021 12:15:14: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 11 Dec 2021 12:15:14: start model_add_line... INFO @ Sat, 11 Dec 2021 12:15:14: start X-correlation... INFO @ Sat, 11 Dec 2021 12:15:14: end of X-cor INFO @ Sat, 11 Dec 2021 12:15:14: #2 finished! INFO @ Sat, 11 Dec 2021 12:15:14: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 12:15:14: #2 alternative fragment length(s) may be 4,154,168,580 bps INFO @ Sat, 11 Dec 2021 12:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.10_model.r WARNING @ Sat, 11 Dec 2021 12:15:14: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:15:14: #2 You may need to consider one of the other alternative d(s): 4,154,168,580 WARNING @ Sat, 11 Dec 2021 12:15:14: #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 12:15:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:15:19: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:15:24: 26000000 INFO @ Sat, 11 Dec 2021 12:15:29: 27000000 INFO @ Sat, 11 Dec 2021 12:15:34: 28000000 INFO @ Sat, 11 Dec 2021 12:15:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:15:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:15:39: 29000000 INFO @ Sat, 11 Dec 2021 12:15:41: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:15:41: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:15:41: #1 total tags in treatment: 12442886 INFO @ Sat, 11 Dec 2021 12:15:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:15:41: #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 12:15:41: #1 tags after filtering in treatment: 11589727 INFO @ Sat, 11 Dec 2021 12:15:41: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 12:15:41: #1 finished! INFO @ Sat, 11 Dec 2021 12:15:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:15:42: #2 number of paired peaks: 108 WARNING @ Sat, 11 Dec 2021 12:15:42: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sat, 11 Dec 2021 12:15:42: start model_add_line... INFO @ Sat, 11 Dec 2021 12:15:42: start X-correlation... INFO @ Sat, 11 Dec 2021 12:15:42: end of X-cor INFO @ Sat, 11 Dec 2021 12:15:42: #2 finished! INFO @ Sat, 11 Dec 2021 12:15:42: #2 predicted fragment length is 154 bps INFO @ Sat, 11 Dec 2021 12:15:42: #2 alternative fragment length(s) may be 4,154,168,580 bps INFO @ Sat, 11 Dec 2021 12:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.20_model.r WARNING @ Sat, 11 Dec 2021 12:15:42: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:15:42: #2 You may need to consider one of the other alternative d(s): 4,154,168,580 WARNING @ Sat, 11 Dec 2021 12:15:42: #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 12:15:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:15:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:15:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:15:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.05_summits.bed INFO @ Sat, 11 Dec 2021 12:15:47: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.10_summits.bed INFO @ Sat, 11 Dec 2021 12:15:48: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:16:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:16:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:16:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:16:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9711630/SRX9711630.20_summits.bed INFO @ Sat, 11 Dec 2021 12:16:15: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。