Job ID = 12265560 SRX = SRX7277024 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25974779 spots for SRR10597289/SRR10597289.sra Written 25974779 spots for SRR10597289/SRR10597289.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265859 ("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: 00:42:10 25974779 reads; of these: 25974779 (100.00%) were paired; of these: 10225143 (39.37%) aligned concordantly 0 times 11002038 (42.36%) aligned concordantly exactly 1 time 4747598 (18.28%) aligned concordantly >1 times ---- 10225143 pairs aligned concordantly 0 times; of these: 2683231 (26.24%) aligned discordantly 1 time ---- 7541912 pairs aligned 0 times concordantly or discordantly; of these: 15083824 mates make up the pairs; of these: 12281686 (81.42%) aligned 0 times 726152 (4.81%) aligned exactly 1 time 2075986 (13.76%) aligned >1 times 76.36% overall alignment rate Time searching: 00:42:10 Overall time: 00:42:10 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] 3151182 / 18296180 = 0.1722 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 08:35:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.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 08:35:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:35:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:36:03: 1000000 INFO @ Sat, 03 Apr 2021 08:36:10: 2000000 INFO @ Sat, 03 Apr 2021 08:36:17: 3000000 INFO @ Sat, 03 Apr 2021 08:36:24: 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 08:36:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.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 08:36:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:36:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:36:30: 5000000 INFO @ Sat, 03 Apr 2021 08:36:32: 1000000 INFO @ Sat, 03 Apr 2021 08:36:37: 6000000 INFO @ Sat, 03 Apr 2021 08:36:38: 2000000 INFO @ Sat, 03 Apr 2021 08:36:44: 7000000 INFO @ Sat, 03 Apr 2021 08:36:45: 3000000 INFO @ Sat, 03 Apr 2021 08:36:51: 4000000 INFO @ Sat, 03 Apr 2021 08:36:51: 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 08:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.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 08:36:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:36:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:36:57: 5000000 INFO @ Sat, 03 Apr 2021 08:36:58: 9000000 INFO @ Sat, 03 Apr 2021 08:37:03: 6000000 INFO @ Sat, 03 Apr 2021 08:37:04: 1000000 INFO @ Sat, 03 Apr 2021 08:37:05: 10000000 INFO @ Sat, 03 Apr 2021 08:37:09: 7000000 INFO @ Sat, 03 Apr 2021 08:37:11: 2000000 INFO @ Sat, 03 Apr 2021 08:37:11: 11000000 INFO @ Sat, 03 Apr 2021 08:37:15: 8000000 INFO @ Sat, 03 Apr 2021 08:37:18: 3000000 INFO @ Sat, 03 Apr 2021 08:37:18: 12000000 INFO @ Sat, 03 Apr 2021 08:37:21: 9000000 INFO @ Sat, 03 Apr 2021 08:37:25: 13000000 INFO @ Sat, 03 Apr 2021 08:37:25: 4000000 INFO @ Sat, 03 Apr 2021 08:37:27: 10000000 INFO @ Sat, 03 Apr 2021 08:37:32: 14000000 INFO @ Sat, 03 Apr 2021 08:37:32: 5000000 INFO @ Sat, 03 Apr 2021 08:37:33: 11000000 INFO @ Sat, 03 Apr 2021 08:37:38: 15000000 INFO @ Sat, 03 Apr 2021 08:37:39: 12000000 INFO @ Sat, 03 Apr 2021 08:37:39: 6000000 INFO @ Sat, 03 Apr 2021 08:37:45: 16000000 INFO @ Sat, 03 Apr 2021 08:37:45: 13000000 INFO @ Sat, 03 Apr 2021 08:37:46: 7000000 INFO @ Sat, 03 Apr 2021 08:37:51: 14000000 INFO @ Sat, 03 Apr 2021 08:37:52: 17000000 INFO @ Sat, 03 Apr 2021 08:37:53: 8000000 INFO @ Sat, 03 Apr 2021 08:37:57: 15000000 INFO @ Sat, 03 Apr 2021 08:37:58: 18000000 INFO @ Sat, 03 Apr 2021 08:38:00: 9000000 INFO @ Sat, 03 Apr 2021 08:38:03: 16000000 INFO @ Sat, 03 Apr 2021 08:38:05: 19000000 INFO @ Sat, 03 Apr 2021 08:38:07: 10000000 INFO @ Sat, 03 Apr 2021 08:38:09: 17000000 INFO @ Sat, 03 Apr 2021 08:38:12: 20000000 INFO @ Sat, 03 Apr 2021 08:38:14: 11000000 INFO @ Sat, 03 Apr 2021 08:38:15: 18000000 INFO @ Sat, 03 Apr 2021 08:38:19: 21000000 INFO @ Sat, 03 Apr 2021 08:38:21: 12000000 INFO @ Sat, 03 Apr 2021 08:38:21: 19000000 INFO @ Sat, 03 Apr 2021 08:38:26: 22000000 INFO @ Sat, 03 Apr 2021 08:38:27: 13000000 INFO @ Sat, 03 Apr 2021 08:38:27: 20000000 INFO @ Sat, 03 Apr 2021 08:38:33: 23000000 INFO @ Sat, 03 Apr 2021 08:38:34: 21000000 INFO @ Sat, 03 Apr 2021 08:38:34: 14000000 INFO @ Sat, 03 Apr 2021 08:38:39: 24000000 INFO @ Sat, 03 Apr 2021 08:38:40: 22000000 INFO @ Sat, 03 Apr 2021 08:38:41: 15000000 INFO @ Sat, 03 Apr 2021 08:38:46: 23000000 INFO @ Sat, 03 Apr 2021 08:38:46: 25000000 INFO @ Sat, 03 Apr 2021 08:38:47: 16000000 INFO @ Sat, 03 Apr 2021 08:38:52: 24000000 INFO @ Sat, 03 Apr 2021 08:38:53: 26000000 INFO @ Sat, 03 Apr 2021 08:38:54: 17000000 INFO @ Sat, 03 Apr 2021 08:38:58: 25000000 INFO @ Sat, 03 Apr 2021 08:39:00: 27000000 INFO @ Sat, 03 Apr 2021 08:39:01: 18000000 INFO @ Sat, 03 Apr 2021 08:39:03: 26000000 INFO @ Sat, 03 Apr 2021 08:39:08: 19000000 INFO @ Sat, 03 Apr 2021 08:39:08: 28000000 INFO @ Sat, 03 Apr 2021 08:39:09: 27000000 INFO @ Sat, 03 Apr 2021 08:39:14: 20000000 INFO @ Sat, 03 Apr 2021 08:39:14: 29000000 INFO @ Sat, 03 Apr 2021 08:39:15: 28000000 INFO @ Sat, 03 Apr 2021 08:39:21: 21000000 INFO @ Sat, 03 Apr 2021 08:39:21: 29000000 INFO @ Sat, 03 Apr 2021 08:39:21: 30000000 INFO @ Sat, 03 Apr 2021 08:39:27: 30000000 INFO @ Sat, 03 Apr 2021 08:39:28: 22000000 INFO @ Sat, 03 Apr 2021 08:39:28: 31000000 INFO @ Sat, 03 Apr 2021 08:39:33: 31000000 INFO @ Sat, 03 Apr 2021 08:39:35: 23000000 INFO @ Sat, 03 Apr 2021 08:39:35: 32000000 INFO @ Sat, 03 Apr 2021 08:39:39: 32000000 INFO @ Sat, 03 Apr 2021 08:39:41: 24000000 INFO @ Sat, 03 Apr 2021 08:39:42: 33000000 INFO @ Sat, 03 Apr 2021 08:39:45: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:39:45: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:39:45: #1 total tags in treatment: 12779573 INFO @ Sat, 03 Apr 2021 08:39:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:39:45: #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 08:39:45: 33000000 INFO @ Sat, 03 Apr 2021 08:39:45: #1 tags after filtering in treatment: 10238552 INFO @ Sat, 03 Apr 2021 08:39:45: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 08:39:45: #1 finished! INFO @ Sat, 03 Apr 2021 08:39:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:39:46: #2 number of paired peaks: 415 WARNING @ Sat, 03 Apr 2021 08:39:46: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sat, 03 Apr 2021 08:39:46: start model_add_line... INFO @ Sat, 03 Apr 2021 08:39:46: start X-correlation... INFO @ Sat, 03 Apr 2021 08:39:46: end of X-cor INFO @ Sat, 03 Apr 2021 08:39:46: #2 finished! INFO @ Sat, 03 Apr 2021 08:39:46: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 08:39:46: #2 alternative fragment length(s) may be 4,86 bps INFO @ Sat, 03 Apr 2021 08:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.05_model.r WARNING @ Sat, 03 Apr 2021 08:39:46: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:39:46: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Sat, 03 Apr 2021 08:39:46: #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 08:39:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:39:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:39:47: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:39:47: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:39:47: #1 total tags in treatment: 12779573 INFO @ Sat, 03 Apr 2021 08:39:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:39:47: #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 08:39:48: #1 tags after filtering in treatment: 10238552 INFO @ Sat, 03 Apr 2021 08:39:48: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 08:39:48: #1 finished! INFO @ Sat, 03 Apr 2021 08:39:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:39:48: 25000000 INFO @ Sat, 03 Apr 2021 08:39:49: #2 number of paired peaks: 415 WARNING @ Sat, 03 Apr 2021 08:39:49: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sat, 03 Apr 2021 08:39:49: start model_add_line... INFO @ Sat, 03 Apr 2021 08:39:49: start X-correlation... INFO @ Sat, 03 Apr 2021 08:39:49: end of X-cor INFO @ Sat, 03 Apr 2021 08:39:49: #2 finished! INFO @ Sat, 03 Apr 2021 08:39:49: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 08:39:49: #2 alternative fragment length(s) may be 4,86 bps INFO @ Sat, 03 Apr 2021 08:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.10_model.r WARNING @ Sat, 03 Apr 2021 08:39:49: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:39:49: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Sat, 03 Apr 2021 08:39:49: #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 08:39:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:39:54: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:40:01: 27000000 INFO @ Sat, 03 Apr 2021 08:40:08: 28000000 INFO @ Sat, 03 Apr 2021 08:40:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:40:14: 29000000 INFO @ Sat, 03 Apr 2021 08:40:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:40:21: 30000000 INFO @ Sat, 03 Apr 2021 08:40:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:40:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:40:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.05_summits.bed INFO @ Sat, 03 Apr 2021 08:40:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6382 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:40:27: 31000000 INFO @ Sat, 03 Apr 2021 08:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.10_summits.bed INFO @ Sat, 03 Apr 2021 08:40:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:40:33: 32000000 INFO @ Sat, 03 Apr 2021 08:40:40: 33000000 INFO @ Sat, 03 Apr 2021 08:40:42: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:40:42: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:40:42: #1 total tags in treatment: 12779573 INFO @ Sat, 03 Apr 2021 08:40:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:40:42: #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 08:40:43: #1 tags after filtering in treatment: 10238552 INFO @ Sat, 03 Apr 2021 08:40:43: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 08:40:43: #1 finished! INFO @ Sat, 03 Apr 2021 08:40:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:40:43: #2 number of paired peaks: 415 WARNING @ Sat, 03 Apr 2021 08:40:43: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sat, 03 Apr 2021 08:40:43: start model_add_line... INFO @ Sat, 03 Apr 2021 08:40:44: start X-correlation... INFO @ Sat, 03 Apr 2021 08:40:44: end of X-cor INFO @ Sat, 03 Apr 2021 08:40:44: #2 finished! INFO @ Sat, 03 Apr 2021 08:40:44: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 08:40:44: #2 alternative fragment length(s) may be 4,86 bps INFO @ Sat, 03 Apr 2021 08:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.20_model.r WARNING @ Sat, 03 Apr 2021 08:40:44: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:40:44: #2 You may need to consider one of the other alternative d(s): 4,86 WARNING @ Sat, 03 Apr 2021 08:40:44: #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 08:40:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:40:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:41:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277024/SRX7277024.20_summits.bed INFO @ Sat, 03 Apr 2021 08:41:23: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 2 millis CompletedMACS2peakCalling