Job ID = 12266617 SRX = SRX7351028 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28927651 spots for SRR10673658/SRR10673658.sra Written 28927651 spots for SRR10673658/SRR10673658.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267989 ("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: 01:14:26 28927651 reads; of these: 28927651 (100.00%) were paired; of these: 12177633 (42.10%) aligned concordantly 0 times 10471424 (36.20%) aligned concordantly exactly 1 time 6278594 (21.70%) aligned concordantly >1 times ---- 12177633 pairs aligned concordantly 0 times; of these: 2315482 (19.01%) aligned discordantly 1 time ---- 9862151 pairs aligned 0 times concordantly or discordantly; of these: 19724302 mates make up the pairs; of these: 16469033 (83.50%) aligned 0 times 716251 (3.63%) aligned exactly 1 time 2539018 (12.87%) aligned >1 times 71.53% overall alignment rate Time searching: 01:14:26 Overall time: 01:14:26 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] 2703245 / 18831167 = 0.1436 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 10:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.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 10:33:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:33:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:33:38: 1000000 INFO @ Sat, 03 Apr 2021 10:33:44: 2000000 INFO @ Sat, 03 Apr 2021 10:33:51: 3000000 INFO @ Sat, 03 Apr 2021 10:33:57: 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 10:34:02: 5000000 INFO @ Sat, 03 Apr 2021 10:34:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.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 10:34:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:34:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:34:08: 6000000 INFO @ Sat, 03 Apr 2021 10:34:08: 1000000 INFO @ Sat, 03 Apr 2021 10:34:13: 7000000 INFO @ Sat, 03 Apr 2021 10:34:14: 2000000 INFO @ Sat, 03 Apr 2021 10:34:19: 8000000 INFO @ Sat, 03 Apr 2021 10:34:20: 3000000 INFO @ Sat, 03 Apr 2021 10:34:24: 9000000 INFO @ Sat, 03 Apr 2021 10:34:25: 4000000 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 10:34:30: 10000000 INFO @ Sat, 03 Apr 2021 10:34:31: 5000000 INFO @ Sat, 03 Apr 2021 10:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.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 10:34:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:34:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:34:36: 11000000 INFO @ Sat, 03 Apr 2021 10:34:37: 6000000 INFO @ Sat, 03 Apr 2021 10:34:37: 1000000 INFO @ Sat, 03 Apr 2021 10:34:42: 12000000 INFO @ Sat, 03 Apr 2021 10:34:42: 7000000 INFO @ Sat, 03 Apr 2021 10:34:43: 2000000 INFO @ Sat, 03 Apr 2021 10:34:48: 13000000 INFO @ Sat, 03 Apr 2021 10:34:49: 8000000 INFO @ Sat, 03 Apr 2021 10:34:50: 3000000 INFO @ Sat, 03 Apr 2021 10:34:54: 14000000 INFO @ Sat, 03 Apr 2021 10:34:54: 9000000 INFO @ Sat, 03 Apr 2021 10:34:56: 4000000 INFO @ Sat, 03 Apr 2021 10:35:00: 15000000 INFO @ Sat, 03 Apr 2021 10:35:00: 10000000 INFO @ Sat, 03 Apr 2021 10:35:02: 5000000 INFO @ Sat, 03 Apr 2021 10:35:05: 11000000 INFO @ Sat, 03 Apr 2021 10:35:06: 16000000 INFO @ Sat, 03 Apr 2021 10:35:08: 6000000 INFO @ Sat, 03 Apr 2021 10:35:11: 12000000 INFO @ Sat, 03 Apr 2021 10:35:11: 17000000 INFO @ Sat, 03 Apr 2021 10:35:14: 7000000 INFO @ Sat, 03 Apr 2021 10:35:16: 13000000 INFO @ Sat, 03 Apr 2021 10:35:17: 18000000 INFO @ Sat, 03 Apr 2021 10:35:20: 8000000 INFO @ Sat, 03 Apr 2021 10:35:22: 14000000 INFO @ Sat, 03 Apr 2021 10:35:23: 19000000 INFO @ Sat, 03 Apr 2021 10:35:26: 9000000 INFO @ Sat, 03 Apr 2021 10:35:28: 15000000 INFO @ Sat, 03 Apr 2021 10:35:29: 20000000 INFO @ Sat, 03 Apr 2021 10:35:32: 10000000 INFO @ Sat, 03 Apr 2021 10:35:33: 16000000 INFO @ Sat, 03 Apr 2021 10:35:35: 21000000 INFO @ Sat, 03 Apr 2021 10:35:38: 11000000 INFO @ Sat, 03 Apr 2021 10:35:39: 17000000 INFO @ Sat, 03 Apr 2021 10:35:41: 22000000 INFO @ Sat, 03 Apr 2021 10:35:44: 12000000 INFO @ Sat, 03 Apr 2021 10:35:45: 18000000 INFO @ Sat, 03 Apr 2021 10:35:47: 23000000 INFO @ Sat, 03 Apr 2021 10:35:50: 13000000 INFO @ Sat, 03 Apr 2021 10:35:50: 19000000 INFO @ Sat, 03 Apr 2021 10:35:52: 24000000 INFO @ Sat, 03 Apr 2021 10:35:56: 14000000 INFO @ Sat, 03 Apr 2021 10:35:56: 20000000 INFO @ Sat, 03 Apr 2021 10:35:58: 25000000 INFO @ Sat, 03 Apr 2021 10:36:02: 15000000 INFO @ Sat, 03 Apr 2021 10:36:02: 21000000 INFO @ Sat, 03 Apr 2021 10:36:04: 26000000 INFO @ Sat, 03 Apr 2021 10:36:07: 22000000 INFO @ Sat, 03 Apr 2021 10:36:08: 16000000 INFO @ Sat, 03 Apr 2021 10:36:10: 27000000 INFO @ Sat, 03 Apr 2021 10:36:13: 23000000 INFO @ Sat, 03 Apr 2021 10:36:14: 17000000 INFO @ Sat, 03 Apr 2021 10:36:16: 28000000 INFO @ Sat, 03 Apr 2021 10:36:19: 24000000 INFO @ Sat, 03 Apr 2021 10:36:20: 18000000 INFO @ Sat, 03 Apr 2021 10:36:21: 29000000 INFO @ Sat, 03 Apr 2021 10:36:25: 25000000 INFO @ Sat, 03 Apr 2021 10:36:26: 19000000 INFO @ Sat, 03 Apr 2021 10:36:27: 30000000 INFO @ Sat, 03 Apr 2021 10:36:30: 26000000 INFO @ Sat, 03 Apr 2021 10:36:32: 20000000 INFO @ Sat, 03 Apr 2021 10:36:33: 31000000 INFO @ Sat, 03 Apr 2021 10:36:35: 27000000 INFO @ Sat, 03 Apr 2021 10:36:37: 21000000 INFO @ Sat, 03 Apr 2021 10:36:39: 32000000 INFO @ Sat, 03 Apr 2021 10:36:41: 28000000 INFO @ Sat, 03 Apr 2021 10:36:43: 22000000 INFO @ Sat, 03 Apr 2021 10:36:45: 33000000 INFO @ Sat, 03 Apr 2021 10:36:46: 29000000 INFO @ Sat, 03 Apr 2021 10:36:49: 23000000 INFO @ Sat, 03 Apr 2021 10:36:51: 34000000 INFO @ Sat, 03 Apr 2021 10:36:52: 30000000 INFO @ Sat, 03 Apr 2021 10:36:55: 24000000 INFO @ Sat, 03 Apr 2021 10:36:57: 35000000 INFO @ Sat, 03 Apr 2021 10:36:57: 31000000 INFO @ Sat, 03 Apr 2021 10:37:01: 25000000 INFO @ Sat, 03 Apr 2021 10:37:02: 32000000 INFO @ Sat, 03 Apr 2021 10:37:03: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 10:37:03: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 10:37:03: #1 total tags in treatment: 14252498 INFO @ Sat, 03 Apr 2021 10:37:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:37:03: #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 10:37:03: #1 tags after filtering in treatment: 12158584 INFO @ Sat, 03 Apr 2021 10:37:03: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 10:37:03: #1 finished! INFO @ Sat, 03 Apr 2021 10:37:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:37:04: #2 number of paired peaks: 349 WARNING @ Sat, 03 Apr 2021 10:37:04: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 03 Apr 2021 10:37:04: start model_add_line... INFO @ Sat, 03 Apr 2021 10:37:04: start X-correlation... INFO @ Sat, 03 Apr 2021 10:37:04: end of X-cor INFO @ Sat, 03 Apr 2021 10:37:04: #2 finished! INFO @ Sat, 03 Apr 2021 10:37:04: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 10:37:04: #2 alternative fragment length(s) may be 4,127,591 bps INFO @ Sat, 03 Apr 2021 10:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.05_model.r WARNING @ Sat, 03 Apr 2021 10:37:04: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:37:04: #2 You may need to consider one of the other alternative d(s): 4,127,591 WARNING @ Sat, 03 Apr 2021 10:37:04: #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 10:37:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:37:06: 26000000 INFO @ Sat, 03 Apr 2021 10:37:08: 33000000 INFO @ Sat, 03 Apr 2021 10:37:12: 27000000 INFO @ Sat, 03 Apr 2021 10:37:13: 34000000 INFO @ Sat, 03 Apr 2021 10:37:17: 28000000 INFO @ Sat, 03 Apr 2021 10:37:19: 35000000 INFO @ Sat, 03 Apr 2021 10:37:22: 29000000 INFO @ Sat, 03 Apr 2021 10:37:24: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 10:37:24: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 10:37:24: #1 total tags in treatment: 14252498 INFO @ Sat, 03 Apr 2021 10:37:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:37:24: #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 10:37:25: #1 tags after filtering in treatment: 12158584 INFO @ Sat, 03 Apr 2021 10:37:25: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 10:37:25: #1 finished! INFO @ Sat, 03 Apr 2021 10:37:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:37:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:37:26: #2 number of paired peaks: 349 WARNING @ Sat, 03 Apr 2021 10:37:26: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 03 Apr 2021 10:37:26: start model_add_line... INFO @ Sat, 03 Apr 2021 10:37:26: start X-correlation... INFO @ Sat, 03 Apr 2021 10:37:26: end of X-cor INFO @ Sat, 03 Apr 2021 10:37:26: #2 finished! INFO @ Sat, 03 Apr 2021 10:37:26: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 10:37:26: #2 alternative fragment length(s) may be 4,127,591 bps INFO @ Sat, 03 Apr 2021 10:37:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.10_model.r WARNING @ Sat, 03 Apr 2021 10:37:26: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:37:26: #2 You may need to consider one of the other alternative d(s): 4,127,591 WARNING @ Sat, 03 Apr 2021 10:37:26: #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 10:37:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:37:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:37:28: 30000000 INFO @ Sat, 03 Apr 2021 10:37:33: 31000000 INFO @ Sat, 03 Apr 2021 10:37:38: 32000000 INFO @ Sat, 03 Apr 2021 10:37:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.05_peaks.xls INFO @ Sat, 03 Apr 2021 10:37:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.05_summits.bed INFO @ Sat, 03 Apr 2021 10:37:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2769 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:37:44: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 10:37:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:37:49: 34000000 INFO @ Sat, 03 Apr 2021 10:37:54: 35000000 INFO @ Sat, 03 Apr 2021 10:37:59: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 10:37:59: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 10:37:59: #1 total tags in treatment: 14252498 INFO @ Sat, 03 Apr 2021 10:37:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:37:59: #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 10:38:00: #1 tags after filtering in treatment: 12158584 INFO @ Sat, 03 Apr 2021 10:38:00: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 03 Apr 2021 10:38:00: #1 finished! INFO @ Sat, 03 Apr 2021 10:38:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:38:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.10_summits.bed INFO @ Sat, 03 Apr 2021 10:38:00: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1278 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:38:01: #2 number of paired peaks: 349 WARNING @ Sat, 03 Apr 2021 10:38:01: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Sat, 03 Apr 2021 10:38:01: start model_add_line... INFO @ Sat, 03 Apr 2021 10:38:01: start X-correlation... INFO @ Sat, 03 Apr 2021 10:38:01: end of X-cor INFO @ Sat, 03 Apr 2021 10:38:01: #2 finished! INFO @ Sat, 03 Apr 2021 10:38:01: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 10:38:01: #2 alternative fragment length(s) may be 4,127,591 bps INFO @ Sat, 03 Apr 2021 10:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.20_model.r WARNING @ Sat, 03 Apr 2021 10:38:01: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:38:01: #2 You may need to consider one of the other alternative d(s): 4,127,591 WARNING @ Sat, 03 Apr 2021 10:38:01: #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 10:38:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:38:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351028/SRX7351028.20_summits.bed INFO @ Sat, 03 Apr 2021 10:38:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。