Job ID = 14171696 SRX = SRX10386220 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22662317 spots for SRR14009285/SRR14009285.sra Written 22662317 spots for SRR14009285/SRR14009285.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172298 ("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: 00:42:53 22662317 reads; of these: 22662317 (100.00%) were paired; of these: 3612708 (15.94%) aligned concordantly 0 times 12506305 (55.19%) aligned concordantly exactly 1 time 6543304 (28.87%) aligned concordantly >1 times ---- 3612708 pairs aligned concordantly 0 times; of these: 606361 (16.78%) aligned discordantly 1 time ---- 3006347 pairs aligned 0 times concordantly or discordantly; of these: 6012694 mates make up the pairs; of these: 4737158 (78.79%) aligned 0 times 564779 (9.39%) aligned exactly 1 time 710757 (11.82%) aligned >1 times 89.55% overall alignment rate Time searching: 00:42:53 Overall time: 00:42:53 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] 2541504 / 19607594 = 0.1296 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 13:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.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 13:22:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:22:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:22:57: 1000000 INFO @ Sat, 11 Dec 2021 13:23:02: 2000000 INFO @ Sat, 11 Dec 2021 13:23:07: 3000000 INFO @ Sat, 11 Dec 2021 13:23:11: 4000000 INFO @ Sat, 11 Dec 2021 13:23:16: 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 13:23:21: 6000000 INFO @ Sat, 11 Dec 2021 13:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.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 13:23:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:27: 7000000 INFO @ Sat, 11 Dec 2021 13:23:28: 1000000 INFO @ Sat, 11 Dec 2021 13:23:32: 8000000 INFO @ Sat, 11 Dec 2021 13:23:33: 2000000 INFO @ Sat, 11 Dec 2021 13:23:37: 9000000 INFO @ Sat, 11 Dec 2021 13:23:38: 3000000 INFO @ Sat, 11 Dec 2021 13:23:43: 10000000 INFO @ Sat, 11 Dec 2021 13:23:44: 4000000 INFO @ Sat, 11 Dec 2021 13:23:48: 11000000 INFO @ Sat, 11 Dec 2021 13:23:49: 5000000 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 13:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.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 13:23:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:23:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:23:53: 12000000 INFO @ Sat, 11 Dec 2021 13:23:54: 6000000 INFO @ Sat, 11 Dec 2021 13:23:58: 1000000 INFO @ Sat, 11 Dec 2021 13:23:59: 13000000 INFO @ Sat, 11 Dec 2021 13:24:00: 7000000 INFO @ Sat, 11 Dec 2021 13:24:03: 2000000 INFO @ Sat, 11 Dec 2021 13:24:04: 14000000 INFO @ Sat, 11 Dec 2021 13:24:05: 8000000 INFO @ Sat, 11 Dec 2021 13:24:08: 3000000 INFO @ Sat, 11 Dec 2021 13:24:09: 15000000 INFO @ Sat, 11 Dec 2021 13:24:11: 9000000 INFO @ Sat, 11 Dec 2021 13:24:14: 4000000 INFO @ Sat, 11 Dec 2021 13:24:15: 16000000 INFO @ Sat, 11 Dec 2021 13:24:16: 10000000 INFO @ Sat, 11 Dec 2021 13:24:19: 5000000 INFO @ Sat, 11 Dec 2021 13:24:20: 17000000 INFO @ Sat, 11 Dec 2021 13:24:21: 11000000 INFO @ Sat, 11 Dec 2021 13:24:25: 6000000 INFO @ Sat, 11 Dec 2021 13:24:26: 18000000 INFO @ Sat, 11 Dec 2021 13:24:27: 12000000 INFO @ Sat, 11 Dec 2021 13:24:30: 7000000 INFO @ Sat, 11 Dec 2021 13:24:31: 19000000 INFO @ Sat, 11 Dec 2021 13:24:32: 13000000 INFO @ Sat, 11 Dec 2021 13:24:35: 8000000 INFO @ Sat, 11 Dec 2021 13:24:36: 20000000 INFO @ Sat, 11 Dec 2021 13:24:38: 14000000 INFO @ Sat, 11 Dec 2021 13:24:41: 9000000 INFO @ Sat, 11 Dec 2021 13:24:42: 21000000 INFO @ Sat, 11 Dec 2021 13:24:43: 15000000 INFO @ Sat, 11 Dec 2021 13:24:46: 10000000 INFO @ Sat, 11 Dec 2021 13:24:47: 22000000 INFO @ Sat, 11 Dec 2021 13:24:49: 16000000 INFO @ Sat, 11 Dec 2021 13:24:51: 11000000 INFO @ Sat, 11 Dec 2021 13:24:52: 23000000 INFO @ Sat, 11 Dec 2021 13:24:54: 17000000 INFO @ Sat, 11 Dec 2021 13:24:57: 12000000 INFO @ Sat, 11 Dec 2021 13:24:58: 24000000 INFO @ Sat, 11 Dec 2021 13:25:00: 18000000 INFO @ Sat, 11 Dec 2021 13:25:02: 13000000 INFO @ Sat, 11 Dec 2021 13:25:03: 25000000 INFO @ Sat, 11 Dec 2021 13:25:05: 19000000 INFO @ Sat, 11 Dec 2021 13:25:07: 14000000 INFO @ Sat, 11 Dec 2021 13:25:09: 26000000 INFO @ Sat, 11 Dec 2021 13:25:11: 20000000 INFO @ Sat, 11 Dec 2021 13:25:13: 15000000 INFO @ Sat, 11 Dec 2021 13:25:14: 27000000 INFO @ Sat, 11 Dec 2021 13:25:16: 21000000 INFO @ Sat, 11 Dec 2021 13:25:18: 16000000 INFO @ Sat, 11 Dec 2021 13:25:20: 28000000 INFO @ Sat, 11 Dec 2021 13:25:21: 22000000 INFO @ Sat, 11 Dec 2021 13:25:24: 17000000 INFO @ Sat, 11 Dec 2021 13:25:25: 29000000 INFO @ Sat, 11 Dec 2021 13:25:27: 23000000 INFO @ Sat, 11 Dec 2021 13:25:29: 18000000 INFO @ Sat, 11 Dec 2021 13:25:30: 30000000 INFO @ Sat, 11 Dec 2021 13:25:32: 24000000 INFO @ Sat, 11 Dec 2021 13:25:34: 19000000 INFO @ Sat, 11 Dec 2021 13:25:36: 31000000 INFO @ Sat, 11 Dec 2021 13:25:38: 25000000 INFO @ Sat, 11 Dec 2021 13:25:40: 20000000 INFO @ Sat, 11 Dec 2021 13:25:41: 32000000 INFO @ Sat, 11 Dec 2021 13:25:43: 26000000 INFO @ Sat, 11 Dec 2021 13:25:45: 21000000 INFO @ Sat, 11 Dec 2021 13:25:47: 33000000 INFO @ Sat, 11 Dec 2021 13:25:49: 27000000 INFO @ Sat, 11 Dec 2021 13:25:50: 22000000 INFO @ Sat, 11 Dec 2021 13:25:52: 34000000 INFO @ Sat, 11 Dec 2021 13:25:54: 28000000 INFO @ Sat, 11 Dec 2021 13:25:56: 23000000 INFO @ Sat, 11 Dec 2021 13:25:58: 35000000 INFO @ Sat, 11 Dec 2021 13:25:59: 29000000 INFO @ Sat, 11 Dec 2021 13:26:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:26:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:26:00: #1 total tags in treatment: 16523138 INFO @ Sat, 11 Dec 2021 13:26:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:00: #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 13:26:01: #1 tags after filtering in treatment: 13833788 INFO @ Sat, 11 Dec 2021 13:26:01: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:26:01: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:01: 24000000 INFO @ Sat, 11 Dec 2021 13:26:02: #2 number of paired peaks: 173 WARNING @ Sat, 11 Dec 2021 13:26:02: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:02: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:02: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:02: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:02: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:02: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 13:26:02: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 13:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.05_model.r WARNING @ Sat, 11 Dec 2021 13:26:02: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:26:02: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 11 Dec 2021 13:26:02: #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 13:26:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:05: 30000000 INFO @ Sat, 11 Dec 2021 13:26:07: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:26:11: 31000000 INFO @ Sat, 11 Dec 2021 13:26:12: 26000000 INFO @ Sat, 11 Dec 2021 13:26:16: 32000000 INFO @ Sat, 11 Dec 2021 13:26:18: 27000000 INFO @ Sat, 11 Dec 2021 13:26:22: 33000000 INFO @ Sat, 11 Dec 2021 13:26:23: 28000000 INFO @ Sat, 11 Dec 2021 13:26:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:26:27: 34000000 INFO @ Sat, 11 Dec 2021 13:26:29: 29000000 INFO @ Sat, 11 Dec 2021 13:26:33: 35000000 INFO @ Sat, 11 Dec 2021 13:26:35: 30000000 INFO @ Sat, 11 Dec 2021 13:26:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:26:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:26:36: #1 total tags in treatment: 16523138 INFO @ Sat, 11 Dec 2021 13:26:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:26:36: #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 13:26:36: #1 tags after filtering in treatment: 13833788 INFO @ Sat, 11 Dec 2021 13:26:36: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:26:36: #1 finished! INFO @ Sat, 11 Dec 2021 13:26:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:26:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:26:37: #2 number of paired peaks: 173 WARNING @ Sat, 11 Dec 2021 13:26:37: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 11 Dec 2021 13:26:37: start model_add_line... INFO @ Sat, 11 Dec 2021 13:26:37: start X-correlation... INFO @ Sat, 11 Dec 2021 13:26:37: end of X-cor INFO @ Sat, 11 Dec 2021 13:26:37: #2 finished! INFO @ Sat, 11 Dec 2021 13:26:37: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 13:26:37: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 13:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.10_model.r WARNING @ Sat, 11 Dec 2021 13:26:37: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:26:37: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 11 Dec 2021 13:26:37: #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 13:26:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:26:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:26:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:26:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.05_summits.bed INFO @ Sat, 11 Dec 2021 13:26:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1505 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:26:40: 31000000 INFO @ Sat, 11 Dec 2021 13:26:45: 32000000 INFO @ Sat, 11 Dec 2021 13:26:50: 33000000 INFO @ Sat, 11 Dec 2021 13:26:56: 34000000 INFO @ Sat, 11 Dec 2021 13:27:01: 35000000 INFO @ Sat, 11 Dec 2021 13:27:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:27:03: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:27:03: #1 total tags in treatment: 16523138 INFO @ Sat, 11 Dec 2021 13:27:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:27:03: #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 13:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:27:04: #1 tags after filtering in treatment: 13833788 INFO @ Sat, 11 Dec 2021 13:27:04: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:27:04: #1 finished! INFO @ Sat, 11 Dec 2021 13:27:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:27:05: #2 number of paired peaks: 173 WARNING @ Sat, 11 Dec 2021 13:27:05: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 11 Dec 2021 13:27:05: start model_add_line... INFO @ Sat, 11 Dec 2021 13:27:05: start X-correlation... INFO @ Sat, 11 Dec 2021 13:27:05: end of X-cor INFO @ Sat, 11 Dec 2021 13:27:05: #2 finished! INFO @ Sat, 11 Dec 2021 13:27:05: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 13:27:05: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 13:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.20_model.r WARNING @ Sat, 11 Dec 2021 13:27:05: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:27:05: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 11 Dec 2021 13:27:05: #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 13:27:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:27:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.10_summits.bed INFO @ Sat, 11 Dec 2021 13:27:17: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1058 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:27:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:27:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:27:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:27:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386220/SRX10386220.20_summits.bed INFO @ Sat, 11 Dec 2021 13:27:42: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (699 records, 4 fields): 2 millis CompletedMACS2peakCalling