Job ID = 12265543 SRX = SRX7277017 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21418295 spots for SRR10597282/SRR10597282.sra Written 21418295 spots for SRR10597282/SRR10597282.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265785 ("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: 00:29:30 21418295 reads; of these: 21418295 (100.00%) were paired; of these: 10124783 (47.27%) aligned concordantly 0 times 7743116 (36.15%) aligned concordantly exactly 1 time 3550396 (16.58%) aligned concordantly >1 times ---- 10124783 pairs aligned concordantly 0 times; of these: 1870712 (18.48%) aligned discordantly 1 time ---- 8254071 pairs aligned 0 times concordantly or discordantly; of these: 16508142 mates make up the pairs; of these: 14411999 (87.30%) aligned 0 times 555540 (3.37%) aligned exactly 1 time 1540603 (9.33%) aligned >1 times 66.36% overall alignment rate Time searching: 00:29:31 Overall time: 00:29:31 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] 1462707 / 13076911 = 0.1119 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.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, 03 Apr 2021 08:14:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:14:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:14:39: 1000000 INFO @ Sat, 03 Apr 2021 08:14:45: 2000000 INFO @ Sat, 03 Apr 2021 08:14:52: 3000000 INFO @ Sat, 03 Apr 2021 08:14:58: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.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, 03 Apr 2021 08:15:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:15:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:15:05: 5000000 INFO @ Sat, 03 Apr 2021 08:15:09: 1000000 INFO @ Sat, 03 Apr 2021 08:15:12: 6000000 INFO @ Sat, 03 Apr 2021 08:15:16: 2000000 INFO @ Sat, 03 Apr 2021 08:15:20: 7000000 INFO @ Sat, 03 Apr 2021 08:15:24: 3000000 INFO @ Sat, 03 Apr 2021 08:15:27: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:15:31: 4000000 INFO @ Sat, 03 Apr 2021 08:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.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, 03 Apr 2021 08:15:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:15:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:15:34: 9000000 INFO @ Sat, 03 Apr 2021 08:15:38: 5000000 INFO @ Sat, 03 Apr 2021 08:15:40: 1000000 INFO @ Sat, 03 Apr 2021 08:15:42: 10000000 INFO @ Sat, 03 Apr 2021 08:15:46: 6000000 INFO @ Sat, 03 Apr 2021 08:15:47: 2000000 INFO @ Sat, 03 Apr 2021 08:15:49: 11000000 INFO @ Sat, 03 Apr 2021 08:15:53: 7000000 INFO @ Sat, 03 Apr 2021 08:15:55: 3000000 INFO @ Sat, 03 Apr 2021 08:15:57: 12000000 INFO @ Sat, 03 Apr 2021 08:16:00: 8000000 INFO @ Sat, 03 Apr 2021 08:16:02: 4000000 INFO @ Sat, 03 Apr 2021 08:16:04: 13000000 INFO @ Sat, 03 Apr 2021 08:16:08: 9000000 INFO @ Sat, 03 Apr 2021 08:16:10: 5000000 INFO @ Sat, 03 Apr 2021 08:16:12: 14000000 INFO @ Sat, 03 Apr 2021 08:16:15: 10000000 INFO @ Sat, 03 Apr 2021 08:16:17: 6000000 INFO @ Sat, 03 Apr 2021 08:16:19: 15000000 INFO @ Sat, 03 Apr 2021 08:16:23: 11000000 INFO @ Sat, 03 Apr 2021 08:16:25: 7000000 INFO @ Sat, 03 Apr 2021 08:16:26: 16000000 INFO @ Sat, 03 Apr 2021 08:16:30: 12000000 INFO @ Sat, 03 Apr 2021 08:16:32: 8000000 INFO @ Sat, 03 Apr 2021 08:16:34: 17000000 INFO @ Sat, 03 Apr 2021 08:16:38: 13000000 INFO @ Sat, 03 Apr 2021 08:16:40: 9000000 INFO @ Sat, 03 Apr 2021 08:16:41: 18000000 INFO @ Sat, 03 Apr 2021 08:16:45: 14000000 INFO @ Sat, 03 Apr 2021 08:16:47: 10000000 INFO @ Sat, 03 Apr 2021 08:16:48: 19000000 INFO @ Sat, 03 Apr 2021 08:16:53: 15000000 INFO @ Sat, 03 Apr 2021 08:16:55: 11000000 INFO @ Sat, 03 Apr 2021 08:16:56: 20000000 INFO @ Sat, 03 Apr 2021 08:17:00: 16000000 INFO @ Sat, 03 Apr 2021 08:17:02: 12000000 INFO @ Sat, 03 Apr 2021 08:17:03: 21000000 INFO @ Sat, 03 Apr 2021 08:17:08: 17000000 INFO @ Sat, 03 Apr 2021 08:17:10: 13000000 INFO @ Sat, 03 Apr 2021 08:17:10: 22000000 INFO @ Sat, 03 Apr 2021 08:17:15: 18000000 INFO @ Sat, 03 Apr 2021 08:17:17: 14000000 INFO @ Sat, 03 Apr 2021 08:17:18: 23000000 INFO @ Sat, 03 Apr 2021 08:17:22: 19000000 INFO @ Sat, 03 Apr 2021 08:17:25: 15000000 INFO @ Sat, 03 Apr 2021 08:17:25: 24000000 INFO @ Sat, 03 Apr 2021 08:17:30: 20000000 INFO @ Sat, 03 Apr 2021 08:17:32: 16000000 INFO @ Sat, 03 Apr 2021 08:17:33: 25000000 INFO @ Sat, 03 Apr 2021 08:17:36: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:17:36: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:17:36: #1 total tags in treatment: 9882766 INFO @ Sat, 03 Apr 2021 08:17:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:17:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:17:37: #1 tags after filtering in treatment: 8241151 INFO @ Sat, 03 Apr 2021 08:17:37: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 08:17:37: #1 finished! INFO @ Sat, 03 Apr 2021 08:17:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:17:37: 21000000 INFO @ Sat, 03 Apr 2021 08:17:37: #2 number of paired peaks: 219 WARNING @ Sat, 03 Apr 2021 08:17:37: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 03 Apr 2021 08:17:37: start model_add_line... INFO @ Sat, 03 Apr 2021 08:17:37: start X-correlation... INFO @ Sat, 03 Apr 2021 08:17:37: end of X-cor INFO @ Sat, 03 Apr 2021 08:17:37: #2 finished! INFO @ Sat, 03 Apr 2021 08:17:37: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Apr 2021 08:17:37: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 03 Apr 2021 08:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.05_model.r WARNING @ Sat, 03 Apr 2021 08:17:37: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:17:37: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Sat, 03 Apr 2021 08:17:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:17:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:17:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:17:39: 17000000 INFO @ Sat, 03 Apr 2021 08:17:45: 22000000 INFO @ Sat, 03 Apr 2021 08:17:47: 18000000 INFO @ Sat, 03 Apr 2021 08:17:52: 23000000 INFO @ Sat, 03 Apr 2021 08:17:54: 19000000 INFO @ Sat, 03 Apr 2021 08:17:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:17:59: 24000000 INFO @ Sat, 03 Apr 2021 08:18:01: 20000000 INFO @ Sat, 03 Apr 2021 08:18:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:18:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:18:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.05_summits.bed INFO @ Sat, 03 Apr 2021 08:18:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4566 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:18:07: 25000000 INFO @ Sat, 03 Apr 2021 08:18:08: 21000000 INFO @ Sat, 03 Apr 2021 08:18:10: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:18:10: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:18:10: #1 total tags in treatment: 9882766 INFO @ Sat, 03 Apr 2021 08:18:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:18:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:18:11: #1 tags after filtering in treatment: 8241151 INFO @ Sat, 03 Apr 2021 08:18:11: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 08:18:11: #1 finished! INFO @ Sat, 03 Apr 2021 08:18:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:18:11: #2 number of paired peaks: 219 WARNING @ Sat, 03 Apr 2021 08:18:11: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 03 Apr 2021 08:18:11: start model_add_line... INFO @ Sat, 03 Apr 2021 08:18:11: start X-correlation... INFO @ Sat, 03 Apr 2021 08:18:11: end of X-cor INFO @ Sat, 03 Apr 2021 08:18:11: #2 finished! INFO @ Sat, 03 Apr 2021 08:18:11: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Apr 2021 08:18:11: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 03 Apr 2021 08:18:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.10_model.r WARNING @ Sat, 03 Apr 2021 08:18:11: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:18:11: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Sat, 03 Apr 2021 08:18:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:18:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:18:15: 22000000 INFO @ Sat, 03 Apr 2021 08:18:22: 23000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:18:29: 24000000 INFO @ Sat, 03 Apr 2021 08:18:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:18:36: 25000000 INFO @ Sat, 03 Apr 2021 08:18:39: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:18:39: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:18:39: #1 total tags in treatment: 9882766 INFO @ Sat, 03 Apr 2021 08:18:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:18:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:18:39: #1 tags after filtering in treatment: 8241151 INFO @ Sat, 03 Apr 2021 08:18:39: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 08:18:39: #1 finished! INFO @ Sat, 03 Apr 2021 08:18:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:18:40: #2 number of paired peaks: 219 WARNING @ Sat, 03 Apr 2021 08:18:40: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 03 Apr 2021 08:18:40: start model_add_line... INFO @ Sat, 03 Apr 2021 08:18:40: start X-correlation... INFO @ Sat, 03 Apr 2021 08:18:40: end of X-cor INFO @ Sat, 03 Apr 2021 08:18:40: #2 finished! INFO @ Sat, 03 Apr 2021 08:18:40: #2 predicted fragment length is 129 bps INFO @ Sat, 03 Apr 2021 08:18:40: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 03 Apr 2021 08:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.20_model.r WARNING @ Sat, 03 Apr 2021 08:18:40: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:18:40: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Sat, 03 Apr 2021 08:18:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:18:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.10_summits.bed INFO @ Sat, 03 Apr 2021 08:18:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1213 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:18:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277017/SRX7277017.20_summits.bed INFO @ Sat, 03 Apr 2021 08:19:09: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 1 millis CompletedMACS2peakCalling