Job ID = 12265390 SRX = SRX6817543 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 50287726 spots for SRR10084534/SRR10084534.sra Written 50287726 spots for SRR10084534/SRR10084534.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266790 ("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: 01:57:03 50287726 reads; of these: 50287726 (100.00%) were paired; of these: 34068102 (67.75%) aligned concordantly 0 times 12866721 (25.59%) aligned concordantly exactly 1 time 3352903 (6.67%) aligned concordantly >1 times ---- 34068102 pairs aligned concordantly 0 times; of these: 3378491 (9.92%) aligned discordantly 1 time ---- 30689611 pairs aligned 0 times concordantly or discordantly; of these: 61379222 mates make up the pairs; of these: 58096780 (94.65%) aligned 0 times 847443 (1.38%) aligned exactly 1 time 2434999 (3.97%) aligned >1 times 42.24% overall alignment rate Time searching: 01:57:03 Overall time: 01:57:03 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 32 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] 3638702 / 19365423 = 0.1879 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 09:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.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 09:29:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:29:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:29:28: 1000000 INFO @ Sat, 03 Apr 2021 09:29:37: 2000000 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 09:29:47: 3000000 INFO @ Sat, 03 Apr 2021 09:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.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 09:29:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:29:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:29:57: 4000000 INFO @ Sat, 03 Apr 2021 09:29:58: 1000000 INFO @ Sat, 03 Apr 2021 09:30:06: 5000000 INFO @ Sat, 03 Apr 2021 09:30:08: 2000000 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 09:30:16: 6000000 INFO @ Sat, 03 Apr 2021 09:30:17: 3000000 INFO @ Sat, 03 Apr 2021 09:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.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 09:30:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:30:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:30:26: 7000000 INFO @ Sat, 03 Apr 2021 09:30:27: 1000000 INFO @ Sat, 03 Apr 2021 09:30:27: 4000000 INFO @ Sat, 03 Apr 2021 09:30:35: 2000000 INFO @ Sat, 03 Apr 2021 09:30:36: 8000000 INFO @ Sat, 03 Apr 2021 09:30:37: 5000000 INFO @ Sat, 03 Apr 2021 09:30:44: 3000000 INFO @ Sat, 03 Apr 2021 09:30:46: 9000000 INFO @ Sat, 03 Apr 2021 09:30:47: 6000000 INFO @ Sat, 03 Apr 2021 09:30:53: 4000000 INFO @ Sat, 03 Apr 2021 09:30:56: 10000000 INFO @ Sat, 03 Apr 2021 09:30:57: 7000000 INFO @ Sat, 03 Apr 2021 09:31:01: 5000000 INFO @ Sat, 03 Apr 2021 09:31:06: 11000000 INFO @ Sat, 03 Apr 2021 09:31:07: 8000000 INFO @ Sat, 03 Apr 2021 09:31:10: 6000000 INFO @ Sat, 03 Apr 2021 09:31:16: 12000000 INFO @ Sat, 03 Apr 2021 09:31:17: 9000000 INFO @ Sat, 03 Apr 2021 09:31:19: 7000000 INFO @ Sat, 03 Apr 2021 09:31:26: 13000000 INFO @ Sat, 03 Apr 2021 09:31:27: 10000000 INFO @ Sat, 03 Apr 2021 09:31:28: 8000000 INFO @ Sat, 03 Apr 2021 09:31:36: 14000000 INFO @ Sat, 03 Apr 2021 09:31:37: 9000000 INFO @ Sat, 03 Apr 2021 09:31:37: 11000000 INFO @ Sat, 03 Apr 2021 09:31:45: 10000000 INFO @ Sat, 03 Apr 2021 09:31:46: 15000000 INFO @ Sat, 03 Apr 2021 09:31:47: 12000000 INFO @ Sat, 03 Apr 2021 09:31:55: 11000000 INFO @ Sat, 03 Apr 2021 09:31:56: 16000000 INFO @ Sat, 03 Apr 2021 09:31:57: 13000000 INFO @ Sat, 03 Apr 2021 09:32:04: 12000000 INFO @ Sat, 03 Apr 2021 09:32:06: 17000000 INFO @ Sat, 03 Apr 2021 09:32:07: 14000000 INFO @ Sat, 03 Apr 2021 09:32:14: 13000000 INFO @ Sat, 03 Apr 2021 09:32:16: 18000000 INFO @ Sat, 03 Apr 2021 09:32:17: 15000000 INFO @ Sat, 03 Apr 2021 09:32:23: 14000000 INFO @ Sat, 03 Apr 2021 09:32:27: 19000000 INFO @ Sat, 03 Apr 2021 09:32:27: 16000000 INFO @ Sat, 03 Apr 2021 09:32:32: 15000000 INFO @ Sat, 03 Apr 2021 09:32:37: 17000000 INFO @ Sat, 03 Apr 2021 09:32:37: 20000000 INFO @ Sat, 03 Apr 2021 09:32:42: 16000000 INFO @ Sat, 03 Apr 2021 09:32:47: 18000000 INFO @ Sat, 03 Apr 2021 09:32:48: 21000000 INFO @ Sat, 03 Apr 2021 09:32:51: 17000000 INFO @ Sat, 03 Apr 2021 09:32:57: 19000000 INFO @ Sat, 03 Apr 2021 09:32:58: 22000000 INFO @ Sat, 03 Apr 2021 09:33:00: 18000000 INFO @ Sat, 03 Apr 2021 09:33:08: 20000000 INFO @ Sat, 03 Apr 2021 09:33:08: 23000000 INFO @ Sat, 03 Apr 2021 09:33:10: 19000000 INFO @ Sat, 03 Apr 2021 09:33:18: 21000000 INFO @ Sat, 03 Apr 2021 09:33:18: 24000000 INFO @ Sat, 03 Apr 2021 09:33:21: 20000000 INFO @ Sat, 03 Apr 2021 09:33:28: 25000000 INFO @ Sat, 03 Apr 2021 09:33:28: 22000000 INFO @ Sat, 03 Apr 2021 09:33:31: 21000000 INFO @ Sat, 03 Apr 2021 09:33:38: 26000000 INFO @ Sat, 03 Apr 2021 09:33:38: 23000000 INFO @ Sat, 03 Apr 2021 09:33:40: 22000000 INFO @ Sat, 03 Apr 2021 09:33:48: 27000000 INFO @ Sat, 03 Apr 2021 09:33:48: 24000000 INFO @ Sat, 03 Apr 2021 09:33:51: 23000000 INFO @ Sat, 03 Apr 2021 09:33:58: 25000000 INFO @ Sat, 03 Apr 2021 09:33:58: 28000000 INFO @ Sat, 03 Apr 2021 09:34:00: 24000000 INFO @ Sat, 03 Apr 2021 09:34:08: 26000000 INFO @ Sat, 03 Apr 2021 09:34:08: 29000000 INFO @ Sat, 03 Apr 2021 09:34:09: 25000000 INFO @ Sat, 03 Apr 2021 09:34:17: 26000000 INFO @ Sat, 03 Apr 2021 09:34:17: 27000000 INFO @ Sat, 03 Apr 2021 09:34:19: 30000000 INFO @ Sat, 03 Apr 2021 09:34:25: 27000000 INFO @ Sat, 03 Apr 2021 09:34:27: 28000000 INFO @ Sat, 03 Apr 2021 09:34:28: 31000000 INFO @ Sat, 03 Apr 2021 09:34:34: 28000000 INFO @ Sat, 03 Apr 2021 09:34:38: 29000000 INFO @ Sat, 03 Apr 2021 09:34:38: 32000000 INFO @ Sat, 03 Apr 2021 09:34:43: 29000000 INFO @ Sat, 03 Apr 2021 09:34:48: 33000000 INFO @ Sat, 03 Apr 2021 09:34:48: 30000000 INFO @ Sat, 03 Apr 2021 09:34:52: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:34:58: 31000000 INFO @ Sat, 03 Apr 2021 09:34:58: 34000000 INFO @ Sat, 03 Apr 2021 09:35:01: 31000000 INFO @ Sat, 03 Apr 2021 09:35:08: 35000000 INFO @ Sat, 03 Apr 2021 09:35:08: 32000000 INFO @ Sat, 03 Apr 2021 09:35:09: 32000000 INFO @ Sat, 03 Apr 2021 09:35:10: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 09:35:10: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 09:35:10: #1 total tags in treatment: 13166710 INFO @ Sat, 03 Apr 2021 09:35:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:35:10: #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 09:35:10: #1 tags after filtering in treatment: 11143341 INFO @ Sat, 03 Apr 2021 09:35:10: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 09:35:10: #1 finished! INFO @ Sat, 03 Apr 2021 09:35:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:35:11: #2 number of paired peaks: 187 WARNING @ Sat, 03 Apr 2021 09:35:11: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 03 Apr 2021 09:35:11: start model_add_line... INFO @ Sat, 03 Apr 2021 09:35:11: start X-correlation... INFO @ Sat, 03 Apr 2021 09:35:11: end of X-cor INFO @ Sat, 03 Apr 2021 09:35:11: #2 finished! INFO @ Sat, 03 Apr 2021 09:35:11: #2 predicted fragment length is 167 bps INFO @ Sat, 03 Apr 2021 09:35:11: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 03 Apr 2021 09:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.05_model.r WARNING @ Sat, 03 Apr 2021 09:35:11: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:35:11: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 03 Apr 2021 09:35:11: #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 09:35:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:35:18: 33000000 INFO @ Sat, 03 Apr 2021 09:35:18: 33000000 INFO @ Sat, 03 Apr 2021 09:35:27: 34000000 INFO @ Sat, 03 Apr 2021 09:35:28: 34000000 INFO @ Sat, 03 Apr 2021 09:35:36: 35000000 INFO @ Sat, 03 Apr 2021 09:35:37: 35000000 INFO @ Sat, 03 Apr 2021 09:35:38: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 09:35:38: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 09:35:38: #1 total tags in treatment: 13166710 INFO @ Sat, 03 Apr 2021 09:35:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:35:38: #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 09:35:38: #1 tags after filtering in treatment: 11143341 INFO @ Sat, 03 Apr 2021 09:35:38: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 09:35:38: #1 finished! INFO @ Sat, 03 Apr 2021 09:35:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:35:39: #2 number of paired peaks: 187 WARNING @ Sat, 03 Apr 2021 09:35:39: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 03 Apr 2021 09:35:39: start model_add_line... INFO @ Sat, 03 Apr 2021 09:35:39: start X-correlation... INFO @ Sat, 03 Apr 2021 09:35:39: end of X-cor INFO @ Sat, 03 Apr 2021 09:35:39: #2 finished! INFO @ Sat, 03 Apr 2021 09:35:39: #2 predicted fragment length is 167 bps INFO @ Sat, 03 Apr 2021 09:35:39: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 03 Apr 2021 09:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.20_model.r WARNING @ Sat, 03 Apr 2021 09:35:39: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:35:39: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 03 Apr 2021 09:35:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:35:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:35:39: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 09:35:39: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 09:35:39: #1 total tags in treatment: 13166710 INFO @ Sat, 03 Apr 2021 09:35:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:35:39: #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 09:35:40: #1 tags after filtering in treatment: 11143341 INFO @ Sat, 03 Apr 2021 09:35:40: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 09:35:40: #1 finished! INFO @ Sat, 03 Apr 2021 09:35:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:35:41: #2 number of paired peaks: 187 WARNING @ Sat, 03 Apr 2021 09:35:41: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sat, 03 Apr 2021 09:35:41: start model_add_line... INFO @ Sat, 03 Apr 2021 09:35:41: start X-correlation... INFO @ Sat, 03 Apr 2021 09:35:41: end of X-cor INFO @ Sat, 03 Apr 2021 09:35:41: #2 finished! INFO @ Sat, 03 Apr 2021 09:35:41: #2 predicted fragment length is 167 bps INFO @ Sat, 03 Apr 2021 09:35:41: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 03 Apr 2021 09:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.10_model.r WARNING @ Sat, 03 Apr 2021 09:35:41: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:35:41: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 03 Apr 2021 09:35:41: #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 09:35:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:35:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:36:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:36:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:36:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.05_summits.bed INFO @ Sat, 03 Apr 2021 09:36:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4886 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:36:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:36:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.20_summits.bed INFO @ Sat, 03 Apr 2021 09:36:29: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:36:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:36:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:36:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817543/SRX6817543.10_summits.bed INFO @ Sat, 03 Apr 2021 09:36:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1370 records, 4 fields): 6 millis CompletedMACS2peakCalling