Job ID = 14170615 SRX = SRX8497060 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14836450 spots for SRR11952659/SRR11952659.sra Written 14836450 spots for SRR11952659/SRR11952659.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171203 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:55:31 14836450 reads; of these: 14836450 (100.00%) were paired; of these: 1936380 (13.05%) aligned concordantly 0 times 9163036 (61.76%) aligned concordantly exactly 1 time 3737034 (25.19%) aligned concordantly >1 times ---- 1936380 pairs aligned concordantly 0 times; of these: 678220 (35.03%) aligned discordantly 1 time ---- 1258160 pairs aligned 0 times concordantly or discordantly; of these: 2516320 mates make up the pairs; of these: 1538154 (61.13%) aligned 0 times 383294 (15.23%) aligned exactly 1 time 594872 (23.64%) aligned >1 times 94.82% overall alignment rate Time searching: 00:55:32 Overall time: 00:55:32 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 12 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] 864334 / 13489766 = 0.0641 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 08:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.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 08:40:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:40:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:40:49: 1000000 INFO @ Sat, 11 Dec 2021 08:41:00: 2000000 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 08:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.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 08:41:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:41:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:41:11: 3000000 INFO @ Sat, 11 Dec 2021 08:41:19: 1000000 INFO @ Sat, 11 Dec 2021 08:41:23: 4000000 INFO @ Sat, 11 Dec 2021 08:41:31: 2000000 INFO @ Sat, 11 Dec 2021 08:41:34: 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 08:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.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 08:41:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:41:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:41:43: 3000000 INFO @ Sat, 11 Dec 2021 08:41:47: 6000000 INFO @ Sat, 11 Dec 2021 08:41:48: 1000000 INFO @ Sat, 11 Dec 2021 08:41:55: 4000000 INFO @ Sat, 11 Dec 2021 08:41:57: 2000000 INFO @ Sat, 11 Dec 2021 08:41:59: 7000000 INFO @ Sat, 11 Dec 2021 08:42:06: 3000000 INFO @ Sat, 11 Dec 2021 08:42:07: 5000000 INFO @ Sat, 11 Dec 2021 08:42:11: 8000000 INFO @ Sat, 11 Dec 2021 08:42:16: 4000000 INFO @ Sat, 11 Dec 2021 08:42:19: 6000000 INFO @ Sat, 11 Dec 2021 08:42:23: 9000000 INFO @ Sat, 11 Dec 2021 08:42:25: 5000000 INFO @ Sat, 11 Dec 2021 08:42:31: 7000000 INFO @ Sat, 11 Dec 2021 08:42:35: 6000000 INFO @ Sat, 11 Dec 2021 08:42:35: 10000000 INFO @ Sat, 11 Dec 2021 08:42:43: 8000000 INFO @ Sat, 11 Dec 2021 08:42:44: 7000000 INFO @ Sat, 11 Dec 2021 08:42:47: 11000000 INFO @ Sat, 11 Dec 2021 08:42:53: 8000000 INFO @ Sat, 11 Dec 2021 08:42:56: 9000000 INFO @ Sat, 11 Dec 2021 08:43:00: 12000000 INFO @ Sat, 11 Dec 2021 08:43:02: 9000000 INFO @ Sat, 11 Dec 2021 08:43:08: 10000000 INFO @ Sat, 11 Dec 2021 08:43:11: 10000000 INFO @ Sat, 11 Dec 2021 08:43:12: 13000000 INFO @ Sat, 11 Dec 2021 08:43:20: 11000000 INFO @ Sat, 11 Dec 2021 08:43:21: 11000000 INFO @ Sat, 11 Dec 2021 08:43:25: 14000000 INFO @ Sat, 11 Dec 2021 08:43:30: 12000000 INFO @ Sat, 11 Dec 2021 08:43:33: 12000000 INFO @ Sat, 11 Dec 2021 08:43:36: 15000000 INFO @ Sat, 11 Dec 2021 08:43:39: 13000000 INFO @ Sat, 11 Dec 2021 08:43:45: 13000000 INFO @ Sat, 11 Dec 2021 08:43:48: 14000000 INFO @ Sat, 11 Dec 2021 08:43:49: 16000000 INFO @ Sat, 11 Dec 2021 08:43:57: 14000000 INFO @ Sat, 11 Dec 2021 08:43:57: 15000000 INFO @ Sat, 11 Dec 2021 08:44:01: 17000000 INFO @ Sat, 11 Dec 2021 08:44:07: 16000000 INFO @ Sat, 11 Dec 2021 08:44:10: 15000000 INFO @ Sat, 11 Dec 2021 08:44:14: 18000000 INFO @ Sat, 11 Dec 2021 08:44:16: 17000000 INFO @ Sat, 11 Dec 2021 08:44:23: 16000000 INFO @ Sat, 11 Dec 2021 08:44:25: 18000000 INFO @ Sat, 11 Dec 2021 08:44:26: 19000000 INFO @ Sat, 11 Dec 2021 08:44:34: 17000000 INFO @ Sat, 11 Dec 2021 08:44:35: 19000000 INFO @ Sat, 11 Dec 2021 08:44:38: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:44:45: 20000000 INFO @ Sat, 11 Dec 2021 08:44:48: 18000000 INFO @ Sat, 11 Dec 2021 08:44:50: 21000000 INFO @ Sat, 11 Dec 2021 08:44:54: 21000000 INFO @ Sat, 11 Dec 2021 08:45:00: 19000000 INFO @ Sat, 11 Dec 2021 08:45:02: 22000000 INFO @ Sat, 11 Dec 2021 08:45:04: 22000000 INFO @ Sat, 11 Dec 2021 08:45:12: 20000000 INFO @ Sat, 11 Dec 2021 08:45:13: 23000000 INFO @ Sat, 11 Dec 2021 08:45:15: 23000000 INFO @ Sat, 11 Dec 2021 08:45:23: 24000000 INFO @ Sat, 11 Dec 2021 08:45:25: 21000000 INFO @ Sat, 11 Dec 2021 08:45:28: 24000000 INFO @ Sat, 11 Dec 2021 08:45:33: 25000000 INFO @ Sat, 11 Dec 2021 08:45:38: 22000000 INFO @ Sat, 11 Dec 2021 08:45:40: 25000000 INFO @ Sat, 11 Dec 2021 08:45:43: 26000000 INFO @ Sat, 11 Dec 2021 08:45:47: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:45:47: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:45:47: #1 total tags in treatment: 12064699 INFO @ Sat, 11 Dec 2021 08:45:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:45:47: #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 08:45:47: #1 tags after filtering in treatment: 11351255 INFO @ Sat, 11 Dec 2021 08:45:47: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:45:47: #1 finished! INFO @ Sat, 11 Dec 2021 08:45:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:45:48: #2 number of paired peaks: 108 WARNING @ Sat, 11 Dec 2021 08:45:48: 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 08:45:48: start model_add_line... INFO @ Sat, 11 Dec 2021 08:45:48: start X-correlation... INFO @ Sat, 11 Dec 2021 08:45:48: end of X-cor INFO @ Sat, 11 Dec 2021 08:45:48: #2 finished! INFO @ Sat, 11 Dec 2021 08:45:48: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Dec 2021 08:45:48: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 11 Dec 2021 08:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.20_model.r WARNING @ Sat, 11 Dec 2021 08:45:48: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:45:48: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 11 Dec 2021 08:45:48: #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 08:45:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:45:50: 23000000 INFO @ Sat, 11 Dec 2021 08:45:53: 26000000 INFO @ Sat, 11 Dec 2021 08:45:57: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:45:57: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:45:57: #1 total tags in treatment: 12064699 INFO @ Sat, 11 Dec 2021 08:45:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:45:57: #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 08:45:58: #1 tags after filtering in treatment: 11351255 INFO @ Sat, 11 Dec 2021 08:45:58: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:45:58: #1 finished! INFO @ Sat, 11 Dec 2021 08:45:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:45:58: #2 number of paired peaks: 108 WARNING @ Sat, 11 Dec 2021 08:45:58: 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 08:45:58: start model_add_line... INFO @ Sat, 11 Dec 2021 08:45:58: start X-correlation... INFO @ Sat, 11 Dec 2021 08:45:58: end of X-cor INFO @ Sat, 11 Dec 2021 08:45:58: #2 finished! INFO @ Sat, 11 Dec 2021 08:45:58: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Dec 2021 08:45:58: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 11 Dec 2021 08:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.05_model.r WARNING @ Sat, 11 Dec 2021 08:45:58: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:45:58: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 11 Dec 2021 08:45:58: #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 08:45:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:46:01: 24000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:46:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:46:11: 25000000 INFO @ Sat, 11 Dec 2021 08:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.20_summits.bed INFO @ Sat, 11 Dec 2021 08:46:22: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (331 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:46:24: 26000000 INFO @ Sat, 11 Dec 2021 08:46:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:46:28: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:46:28: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:46:28: #1 total tags in treatment: 12064699 INFO @ Sat, 11 Dec 2021 08:46:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:46:28: #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 08:46:28: #1 tags after filtering in treatment: 11351255 INFO @ Sat, 11 Dec 2021 08:46:28: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 08:46:28: #1 finished! INFO @ Sat, 11 Dec 2021 08:46:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:46:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:46:29: #2 number of paired peaks: 108 WARNING @ Sat, 11 Dec 2021 08:46:29: 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 08:46:29: start model_add_line... INFO @ Sat, 11 Dec 2021 08:46:29: start X-correlation... INFO @ Sat, 11 Dec 2021 08:46:29: end of X-cor INFO @ Sat, 11 Dec 2021 08:46:29: #2 finished! INFO @ Sat, 11 Dec 2021 08:46:29: #2 predicted fragment length is 139 bps INFO @ Sat, 11 Dec 2021 08:46:29: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 11 Dec 2021 08:46:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.10_model.r WARNING @ Sat, 11 Dec 2021 08:46:29: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:46:29: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 11 Dec 2021 08:46:29: #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 08:46:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:46:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.05_summits.bed INFO @ Sat, 11 Dec 2021 08:46:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1368 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:46:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497060/SRX8497060.10_summits.bed INFO @ Sat, 11 Dec 2021 08:47:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (675 records, 4 fields): 4 millis CompletedMACS2peakCalling