Job ID = 14171523 SRX = SRX10386202 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27295633 spots for SRR14009267/SRR14009267.sra Written 27295633 spots for SRR14009267/SRR14009267.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172379 ("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: 01:29:10 27295633 reads; of these: 27295633 (100.00%) were paired; of these: 8074448 (29.58%) aligned concordantly 0 times 8871811 (32.50%) aligned concordantly exactly 1 time 10349374 (37.92%) aligned concordantly >1 times ---- 8074448 pairs aligned concordantly 0 times; of these: 396984 (4.92%) aligned discordantly 1 time ---- 7677464 pairs aligned 0 times concordantly or discordantly; of these: 15354928 mates make up the pairs; of these: 14438263 (94.03%) aligned 0 times 401034 (2.61%) aligned exactly 1 time 515631 (3.36%) aligned >1 times 73.55% overall alignment rate Time searching: 01:29:11 Overall time: 01:29:11 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] 6527067 / 19509743 = 0.3346 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 13:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.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 13:38:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:38:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:38:30: 1000000 INFO @ Sat, 11 Dec 2021 13:38:38: 2000000 INFO @ Sat, 11 Dec 2021 13:38:46: 3000000 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 13:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.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 13:38:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:38:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:38:54: 4000000 INFO @ Sat, 11 Dec 2021 13:39:01: 1000000 INFO @ Sat, 11 Dec 2021 13:39:02: 5000000 INFO @ Sat, 11 Dec 2021 13:39:09: 2000000 INFO @ Sat, 11 Dec 2021 13:39:10: 6000000 INFO @ Sat, 11 Dec 2021 13:39:17: 3000000 INFO @ Sat, 11 Dec 2021 13:39:18: 7000000 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 13:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.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 13:39:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:39:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:39:26: 4000000 INFO @ Sat, 11 Dec 2021 13:39:27: 8000000 INFO @ Sat, 11 Dec 2021 13:39:31: 1000000 INFO @ Sat, 11 Dec 2021 13:39:34: 5000000 INFO @ Sat, 11 Dec 2021 13:39:35: 9000000 INFO @ Sat, 11 Dec 2021 13:39:39: 2000000 INFO @ Sat, 11 Dec 2021 13:39:43: 6000000 INFO @ Sat, 11 Dec 2021 13:39:44: 10000000 INFO @ Sat, 11 Dec 2021 13:39:47: 3000000 INFO @ Sat, 11 Dec 2021 13:39:52: 7000000 INFO @ Sat, 11 Dec 2021 13:39:52: 11000000 INFO @ Sat, 11 Dec 2021 13:39:56: 4000000 INFO @ Sat, 11 Dec 2021 13:40:00: 8000000 INFO @ Sat, 11 Dec 2021 13:40:01: 12000000 INFO @ Sat, 11 Dec 2021 13:40:04: 5000000 INFO @ Sat, 11 Dec 2021 13:40:09: 9000000 INFO @ Sat, 11 Dec 2021 13:40:09: 13000000 INFO @ Sat, 11 Dec 2021 13:40:12: 6000000 INFO @ Sat, 11 Dec 2021 13:40:17: 10000000 INFO @ Sat, 11 Dec 2021 13:40:18: 14000000 INFO @ Sat, 11 Dec 2021 13:40:20: 7000000 INFO @ Sat, 11 Dec 2021 13:40:25: 11000000 INFO @ Sat, 11 Dec 2021 13:40:26: 15000000 INFO @ Sat, 11 Dec 2021 13:40:28: 8000000 INFO @ Sat, 11 Dec 2021 13:40:34: 12000000 INFO @ Sat, 11 Dec 2021 13:40:34: 16000000 INFO @ Sat, 11 Dec 2021 13:40:37: 9000000 INFO @ Sat, 11 Dec 2021 13:40:42: 13000000 INFO @ Sat, 11 Dec 2021 13:40:43: 17000000 INFO @ Sat, 11 Dec 2021 13:40:45: 10000000 INFO @ Sat, 11 Dec 2021 13:40:50: 14000000 INFO @ Sat, 11 Dec 2021 13:40:51: 18000000 INFO @ Sat, 11 Dec 2021 13:40:54: 11000000 INFO @ Sat, 11 Dec 2021 13:40:58: 15000000 INFO @ Sat, 11 Dec 2021 13:40:59: 19000000 INFO @ Sat, 11 Dec 2021 13:41:02: 12000000 INFO @ Sat, 11 Dec 2021 13:41:07: 16000000 INFO @ Sat, 11 Dec 2021 13:41:07: 20000000 INFO @ Sat, 11 Dec 2021 13:41:10: 13000000 INFO @ Sat, 11 Dec 2021 13:41:15: 17000000 INFO @ Sat, 11 Dec 2021 13:41:16: 21000000 INFO @ Sat, 11 Dec 2021 13:41:18: 14000000 INFO @ Sat, 11 Dec 2021 13:41:23: 18000000 INFO @ Sat, 11 Dec 2021 13:41:24: 22000000 INFO @ Sat, 11 Dec 2021 13:41:26: 15000000 INFO @ Sat, 11 Dec 2021 13:41:32: 19000000 INFO @ Sat, 11 Dec 2021 13:41:32: 23000000 INFO @ Sat, 11 Dec 2021 13:41:34: 16000000 INFO @ Sat, 11 Dec 2021 13:41:40: 20000000 INFO @ Sat, 11 Dec 2021 13:41:40: 24000000 INFO @ Sat, 11 Dec 2021 13:41:42: 17000000 INFO @ Sat, 11 Dec 2021 13:41:48: 21000000 INFO @ Sat, 11 Dec 2021 13:41:49: 25000000 INFO @ Sat, 11 Dec 2021 13:41:51: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:41:57: 22000000 INFO @ Sat, 11 Dec 2021 13:41:57: 26000000 INFO @ Sat, 11 Dec 2021 13:41:59: 19000000 INFO @ Sat, 11 Dec 2021 13:42:05: 27000000 INFO @ Sat, 11 Dec 2021 13:42:05: 23000000 INFO @ Sat, 11 Dec 2021 13:42:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:42:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:42:06: #1 total tags in treatment: 12735982 INFO @ Sat, 11 Dec 2021 13:42:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:42:06: #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 13:42:06: #1 tags after filtering in treatment: 9426880 INFO @ Sat, 11 Dec 2021 13:42:06: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 13:42:06: #1 finished! INFO @ Sat, 11 Dec 2021 13:42:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:42:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:42:07: #2 number of paired peaks: 759 WARNING @ Sat, 11 Dec 2021 13:42:07: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sat, 11 Dec 2021 13:42:07: start model_add_line... INFO @ Sat, 11 Dec 2021 13:42:07: start X-correlation... INFO @ Sat, 11 Dec 2021 13:42:07: end of X-cor INFO @ Sat, 11 Dec 2021 13:42:07: #2 finished! INFO @ Sat, 11 Dec 2021 13:42:07: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 13:42:07: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 11 Dec 2021 13:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.05_model.r WARNING @ Sat, 11 Dec 2021 13:42:07: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:42:07: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sat, 11 Dec 2021 13:42:07: #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 13:42:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:42:07: 20000000 INFO @ Sat, 11 Dec 2021 13:42:13: 24000000 INFO @ Sat, 11 Dec 2021 13:42:15: 21000000 INFO @ Sat, 11 Dec 2021 13:42:21: 25000000 INFO @ Sat, 11 Dec 2021 13:42:23: 22000000 INFO @ Sat, 11 Dec 2021 13:42:29: 26000000 INFO @ Sat, 11 Dec 2021 13:42:31: 23000000 INFO @ Sat, 11 Dec 2021 13:42:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:37: 27000000 INFO @ Sat, 11 Dec 2021 13:42:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:42:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:42:38: #1 total tags in treatment: 12735982 INFO @ Sat, 11 Dec 2021 13:42:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:42:38: #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 13:42:38: #1 tags after filtering in treatment: 9426880 INFO @ Sat, 11 Dec 2021 13:42:38: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 13:42:38: #1 finished! INFO @ Sat, 11 Dec 2021 13:42:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:42:39: #2 number of paired peaks: 759 WARNING @ Sat, 11 Dec 2021 13:42:39: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sat, 11 Dec 2021 13:42:39: start model_add_line... INFO @ Sat, 11 Dec 2021 13:42:39: start X-correlation... INFO @ Sat, 11 Dec 2021 13:42:39: end of X-cor INFO @ Sat, 11 Dec 2021 13:42:39: #2 finished! INFO @ Sat, 11 Dec 2021 13:42:39: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 13:42:39: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 11 Dec 2021 13:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.10_model.r WARNING @ Sat, 11 Dec 2021 13:42:39: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:42:39: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sat, 11 Dec 2021 13:42:39: #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 13:42:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:42:40: 24000000 INFO @ Sat, 11 Dec 2021 13:42:47: 25000000 INFO @ Sat, 11 Dec 2021 13:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:42:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:42:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.05_summits.bed INFO @ Sat, 11 Dec 2021 13:42:47: Done! BigWig に変換しました。 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2291 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:42:55: 26000000 INFO @ Sat, 11 Dec 2021 13:43:03: 27000000 INFO @ Sat, 11 Dec 2021 13:43:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:43:03: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:43:03: #1 total tags in treatment: 12735982 INFO @ Sat, 11 Dec 2021 13:43:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:43:03: #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 13:43:04: #1 tags after filtering in treatment: 9426880 INFO @ Sat, 11 Dec 2021 13:43:04: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 11 Dec 2021 13:43:04: #1 finished! INFO @ Sat, 11 Dec 2021 13:43:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:43:05: #2 number of paired peaks: 759 WARNING @ Sat, 11 Dec 2021 13:43:05: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sat, 11 Dec 2021 13:43:05: start model_add_line... INFO @ Sat, 11 Dec 2021 13:43:05: start X-correlation... INFO @ Sat, 11 Dec 2021 13:43:05: end of X-cor INFO @ Sat, 11 Dec 2021 13:43:05: #2 finished! INFO @ Sat, 11 Dec 2021 13:43:05: #2 predicted fragment length is 88 bps INFO @ Sat, 11 Dec 2021 13:43:05: #2 alternative fragment length(s) may be 88 bps INFO @ Sat, 11 Dec 2021 13:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.20_model.r WARNING @ Sat, 11 Dec 2021 13:43:05: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:43:05: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sat, 11 Dec 2021 13:43:05: #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 13:43:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:43:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:43:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.10_summits.bed INFO @ Sat, 11 Dec 2021 13:43:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1524 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:43:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386202/SRX10386202.20_summits.bed INFO @ Sat, 11 Dec 2021 13:43:46: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1020 records, 4 fields): 5 millis CompletedMACS2peakCalling