Job ID = 12266619 SRX = SRX7351030 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30625545 spots for SRR10673660/SRR10673660.sra Written 30625545 spots for SRR10673660/SRR10673660.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267996 ("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: 01:14:31 30625545 reads; of these: 30625545 (100.00%) were paired; of these: 14015659 (45.76%) aligned concordantly 0 times 10196833 (33.30%) aligned concordantly exactly 1 time 6413053 (20.94%) aligned concordantly >1 times ---- 14015659 pairs aligned concordantly 0 times; of these: 2386195 (17.03%) aligned discordantly 1 time ---- 11629464 pairs aligned 0 times concordantly or discordantly; of these: 23258928 mates make up the pairs; of these: 19608404 (84.30%) aligned 0 times 771775 (3.32%) aligned exactly 1 time 2878749 (12.38%) aligned >1 times 67.99% overall alignment rate Time searching: 01:14:31 Overall time: 01:14:31 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 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] 2926916 / 18766127 = 0.1560 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 10:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.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 10:34:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:34:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:34:46: 1000000 INFO @ Sat, 03 Apr 2021 10:34:52: 2000000 INFO @ Sat, 03 Apr 2021 10:34:59: 3000000 INFO @ Sat, 03 Apr 2021 10:35:05: 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 10:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.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 10:35:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:35:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:35:12: 5000000 INFO @ Sat, 03 Apr 2021 10:35:18: 1000000 INFO @ Sat, 03 Apr 2021 10:35:20: 6000000 INFO @ Sat, 03 Apr 2021 10:35:27: 2000000 INFO @ Sat, 03 Apr 2021 10:35:28: 7000000 INFO @ Sat, 03 Apr 2021 10:35:34: 8000000 INFO @ Sat, 03 Apr 2021 10:35:35: 3000000 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 10:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.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 10:35:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:35:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:35:41: 9000000 INFO @ Sat, 03 Apr 2021 10:35:44: 4000000 INFO @ Sat, 03 Apr 2021 10:35:49: 10000000 INFO @ Sat, 03 Apr 2021 10:35:49: 1000000 INFO @ Sat, 03 Apr 2021 10:35:56: 5000000 INFO @ Sat, 03 Apr 2021 10:35:57: 11000000 INFO @ Sat, 03 Apr 2021 10:35:58: 2000000 INFO @ Sat, 03 Apr 2021 10:36:06: 3000000 INFO @ Sat, 03 Apr 2021 10:36:07: 12000000 INFO @ Sat, 03 Apr 2021 10:36:08: 6000000 INFO @ Sat, 03 Apr 2021 10:36:18: 4000000 INFO @ Sat, 03 Apr 2021 10:36:18: 7000000 INFO @ Sat, 03 Apr 2021 10:36:19: 13000000 INFO @ Sat, 03 Apr 2021 10:36:28: 5000000 INFO @ Sat, 03 Apr 2021 10:36:29: 14000000 INFO @ Sat, 03 Apr 2021 10:36:30: 8000000 INFO @ Sat, 03 Apr 2021 10:36:37: 6000000 INFO @ Sat, 03 Apr 2021 10:36:38: 15000000 INFO @ Sat, 03 Apr 2021 10:36:40: 9000000 INFO @ Sat, 03 Apr 2021 10:36:46: 7000000 INFO @ Sat, 03 Apr 2021 10:36:47: 16000000 INFO @ Sat, 03 Apr 2021 10:36:52: 10000000 INFO @ Sat, 03 Apr 2021 10:36:54: 8000000 INFO @ Sat, 03 Apr 2021 10:36:55: 17000000 INFO @ Sat, 03 Apr 2021 10:37:02: 11000000 INFO @ Sat, 03 Apr 2021 10:37:03: 9000000 INFO @ Sat, 03 Apr 2021 10:37:04: 18000000 INFO @ Sat, 03 Apr 2021 10:37:11: 10000000 INFO @ Sat, 03 Apr 2021 10:37:12: 12000000 INFO @ Sat, 03 Apr 2021 10:37:12: 19000000 INFO @ Sat, 03 Apr 2021 10:37:20: 13000000 INFO @ Sat, 03 Apr 2021 10:37:21: 11000000 INFO @ Sat, 03 Apr 2021 10:37:21: 20000000 INFO @ Sat, 03 Apr 2021 10:37:29: 21000000 INFO @ Sat, 03 Apr 2021 10:37:30: 12000000 INFO @ Sat, 03 Apr 2021 10:37:30: 14000000 INFO @ Sat, 03 Apr 2021 10:37:38: 22000000 INFO @ Sat, 03 Apr 2021 10:37:38: 13000000 INFO @ Sat, 03 Apr 2021 10:37:39: 15000000 INFO @ Sat, 03 Apr 2021 10:37:46: 23000000 INFO @ Sat, 03 Apr 2021 10:37:47: 14000000 INFO @ Sat, 03 Apr 2021 10:37:49: 16000000 INFO @ Sat, 03 Apr 2021 10:37:55: 24000000 INFO @ Sat, 03 Apr 2021 10:37:56: 15000000 INFO @ Sat, 03 Apr 2021 10:37:59: 17000000 INFO @ Sat, 03 Apr 2021 10:38:04: 25000000 INFO @ Sat, 03 Apr 2021 10:38:05: 16000000 INFO @ Sat, 03 Apr 2021 10:38:09: 18000000 INFO @ Sat, 03 Apr 2021 10:38:12: 26000000 INFO @ Sat, 03 Apr 2021 10:38:13: 17000000 INFO @ Sat, 03 Apr 2021 10:38:19: 19000000 INFO @ Sat, 03 Apr 2021 10:38:21: 27000000 INFO @ Sat, 03 Apr 2021 10:38:23: 18000000 INFO @ Sat, 03 Apr 2021 10:38:28: 20000000 INFO @ Sat, 03 Apr 2021 10:38:29: 28000000 INFO @ Sat, 03 Apr 2021 10:38:32: 19000000 INFO @ Sat, 03 Apr 2021 10:38:37: 21000000 INFO @ Sat, 03 Apr 2021 10:38:38: 29000000 INFO @ Sat, 03 Apr 2021 10:38:41: 20000000 INFO @ Sat, 03 Apr 2021 10:38:46: 22000000 INFO @ Sat, 03 Apr 2021 10:38:47: 30000000 INFO @ Sat, 03 Apr 2021 10:38:49: 21000000 INFO @ Sat, 03 Apr 2021 10:38:55: 23000000 INFO @ Sat, 03 Apr 2021 10:38:56: 31000000 INFO @ Sat, 03 Apr 2021 10:38:58: 22000000 INFO @ Sat, 03 Apr 2021 10:39:05: 24000000 INFO @ Sat, 03 Apr 2021 10:39:06: 32000000 INFO @ Sat, 03 Apr 2021 10:39:07: 23000000 INFO @ Sat, 03 Apr 2021 10:39:14: 25000000 INFO @ Sat, 03 Apr 2021 10:39:14: 33000000 INFO @ Sat, 03 Apr 2021 10:39:16: 24000000 INFO @ Sat, 03 Apr 2021 10:39:22: 26000000 INFO @ Sat, 03 Apr 2021 10:39:23: 34000000 INFO @ Sat, 03 Apr 2021 10:39:25: 25000000 INFO @ Sat, 03 Apr 2021 10:39:31: 27000000 INFO @ Sat, 03 Apr 2021 10:39:32: 35000000 INFO @ Sat, 03 Apr 2021 10:39:33: 26000000 INFO @ Sat, 03 Apr 2021 10:39:39: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 10:39:39: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 10:39:39: #1 total tags in treatment: 13895016 INFO @ Sat, 03 Apr 2021 10:39:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:39:39: #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 10:39:39: #1 tags after filtering in treatment: 11676387 INFO @ Sat, 03 Apr 2021 10:39:39: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 10:39:39: #1 finished! INFO @ Sat, 03 Apr 2021 10:39:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:39:40: 28000000 INFO @ Sat, 03 Apr 2021 10:39:40: #2 number of paired peaks: 434 WARNING @ Sat, 03 Apr 2021 10:39:40: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sat, 03 Apr 2021 10:39:40: start model_add_line... INFO @ Sat, 03 Apr 2021 10:39:40: start X-correlation... INFO @ Sat, 03 Apr 2021 10:39:40: end of X-cor INFO @ Sat, 03 Apr 2021 10:39:40: #2 finished! INFO @ Sat, 03 Apr 2021 10:39:40: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 10:39:40: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sat, 03 Apr 2021 10:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.05_model.r WARNING @ Sat, 03 Apr 2021 10:39:40: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:39:40: #2 You may need to consider one of the other alternative d(s): 4,117 WARNING @ Sat, 03 Apr 2021 10:39:40: #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 10:39:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:39:42: 27000000 INFO @ Sat, 03 Apr 2021 10:39:49: 29000000 INFO @ Sat, 03 Apr 2021 10:39:50: 28000000 INFO @ Sat, 03 Apr 2021 10:39:58: 30000000 INFO @ Sat, 03 Apr 2021 10:39:59: 29000000 INFO @ Sat, 03 Apr 2021 10:40:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:40:07: 31000000 INFO @ Sat, 03 Apr 2021 10:40:08: 30000000 INFO @ Sat, 03 Apr 2021 10:40:16: 32000000 INFO @ Sat, 03 Apr 2021 10:40:16: 31000000 INFO @ Sat, 03 Apr 2021 10:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.05_peaks.xls INFO @ Sat, 03 Apr 2021 10:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.05_summits.bed INFO @ Sat, 03 Apr 2021 10:40:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3365 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:40:25: 32000000 INFO @ Sat, 03 Apr 2021 10:40:25: 33000000 INFO @ Sat, 03 Apr 2021 10:40:33: 33000000 INFO @ Sat, 03 Apr 2021 10:40:33: 34000000 INFO @ Sat, 03 Apr 2021 10:40:40: 34000000 INFO @ Sat, 03 Apr 2021 10:40:42: 35000000 INFO @ Sat, 03 Apr 2021 10:40:49: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 10:40:49: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 10:40:49: #1 total tags in treatment: 13895016 INFO @ Sat, 03 Apr 2021 10:40:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:40:49: #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 10:40:50: #1 tags after filtering in treatment: 11676387 INFO @ Sat, 03 Apr 2021 10:40:50: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 10:40:50: #1 finished! INFO @ Sat, 03 Apr 2021 10:40:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:40:50: 35000000 INFO @ Sat, 03 Apr 2021 10:40:50: #2 number of paired peaks: 434 WARNING @ Sat, 03 Apr 2021 10:40:50: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sat, 03 Apr 2021 10:40:50: start model_add_line... INFO @ Sat, 03 Apr 2021 10:40:51: start X-correlation... INFO @ Sat, 03 Apr 2021 10:40:51: end of X-cor INFO @ Sat, 03 Apr 2021 10:40:51: #2 finished! INFO @ Sat, 03 Apr 2021 10:40:51: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 10:40:51: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sat, 03 Apr 2021 10:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.10_model.r WARNING @ Sat, 03 Apr 2021 10:40:51: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:40:51: #2 You may need to consider one of the other alternative d(s): 4,117 WARNING @ Sat, 03 Apr 2021 10:40:51: #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 10:40:51: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:40:57: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 10:40:57: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 10:40:57: #1 total tags in treatment: 13895016 INFO @ Sat, 03 Apr 2021 10:40:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:40:57: #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 10:40:57: #1 tags after filtering in treatment: 11676387 INFO @ Sat, 03 Apr 2021 10:40:57: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 10:40:57: #1 finished! INFO @ Sat, 03 Apr 2021 10:40:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:40:58: #2 number of paired peaks: 434 WARNING @ Sat, 03 Apr 2021 10:40:58: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sat, 03 Apr 2021 10:40:58: start model_add_line... INFO @ Sat, 03 Apr 2021 10:40:58: start X-correlation... INFO @ Sat, 03 Apr 2021 10:40:58: end of X-cor INFO @ Sat, 03 Apr 2021 10:40:58: #2 finished! INFO @ Sat, 03 Apr 2021 10:40:58: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 10:40:58: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sat, 03 Apr 2021 10:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.20_model.r WARNING @ Sat, 03 Apr 2021 10:40:58: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:40:58: #2 You may need to consider one of the other alternative d(s): 4,117 WARNING @ Sat, 03 Apr 2021 10:40:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:40:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:41:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:41:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.10_summits.bed INFO @ Sat, 03 Apr 2021 10:41:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1634 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351030/SRX7351030.20_summits.bed INFO @ Sat, 03 Apr 2021 10:41:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (632 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。