Job ID = 12265611 SRX = SRX7277035 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25528647 spots for SRR10597300/SRR10597300.sra Written 25528647 spots for SRR10597300/SRR10597300.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265912 ("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: 00:35:47 25528647 reads; of these: 25528647 (100.00%) were paired; of these: 10074341 (39.46%) aligned concordantly 0 times 10360955 (40.59%) aligned concordantly exactly 1 time 5093351 (19.95%) aligned concordantly >1 times ---- 10074341 pairs aligned concordantly 0 times; of these: 2636139 (26.17%) aligned discordantly 1 time ---- 7438202 pairs aligned 0 times concordantly or discordantly; of these: 14876404 mates make up the pairs; of these: 11935150 (80.23%) aligned 0 times 735719 (4.95%) aligned exactly 1 time 2205535 (14.83%) aligned >1 times 76.62% overall alignment rate Time searching: 00:35:47 Overall time: 00:35:47 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 16 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] 3206136 / 17947924 = 0.1786 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 08:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.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 08:38:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:38:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:38:56: 1000000 INFO @ Sat, 03 Apr 2021 08:39:03: 2000000 INFO @ Sat, 03 Apr 2021 08:39:09: 3000000 INFO @ Sat, 03 Apr 2021 08:39:16: 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 08:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.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 08:39:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:39:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:39:24: 5000000 INFO @ Sat, 03 Apr 2021 08:39:27: 1000000 INFO @ Sat, 03 Apr 2021 08:39:32: 6000000 INFO @ Sat, 03 Apr 2021 08:39:35: 2000000 INFO @ Sat, 03 Apr 2021 08:39:41: 7000000 INFO @ Sat, 03 Apr 2021 08:39:44: 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 08:39:49: 8000000 INFO @ Sat, 03 Apr 2021 08:39:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.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 08:39:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:39:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:39:52: 4000000 INFO @ Sat, 03 Apr 2021 08:39:57: 1000000 INFO @ Sat, 03 Apr 2021 08:39:57: 9000000 INFO @ Sat, 03 Apr 2021 08:40:00: 5000000 INFO @ Sat, 03 Apr 2021 08:40:05: 2000000 INFO @ Sat, 03 Apr 2021 08:40:05: 10000000 INFO @ Sat, 03 Apr 2021 08:40:08: 6000000 INFO @ Sat, 03 Apr 2021 08:40:13: 3000000 INFO @ Sat, 03 Apr 2021 08:40:14: 11000000 INFO @ Sat, 03 Apr 2021 08:40:16: 7000000 INFO @ Sat, 03 Apr 2021 08:40:21: 4000000 INFO @ Sat, 03 Apr 2021 08:40:22: 12000000 INFO @ Sat, 03 Apr 2021 08:40:25: 8000000 INFO @ Sat, 03 Apr 2021 08:40:29: 5000000 INFO @ Sat, 03 Apr 2021 08:40:30: 13000000 INFO @ Sat, 03 Apr 2021 08:40:33: 9000000 INFO @ Sat, 03 Apr 2021 08:40:37: 6000000 INFO @ Sat, 03 Apr 2021 08:40:38: 14000000 INFO @ Sat, 03 Apr 2021 08:40:41: 10000000 INFO @ Sat, 03 Apr 2021 08:40:45: 7000000 INFO @ Sat, 03 Apr 2021 08:40:47: 15000000 INFO @ Sat, 03 Apr 2021 08:40:49: 11000000 INFO @ Sat, 03 Apr 2021 08:40:53: 8000000 INFO @ Sat, 03 Apr 2021 08:40:55: 16000000 INFO @ Sat, 03 Apr 2021 08:40:57: 12000000 INFO @ Sat, 03 Apr 2021 08:41:00: 9000000 INFO @ Sat, 03 Apr 2021 08:41:03: 17000000 INFO @ Sat, 03 Apr 2021 08:41:06: 13000000 INFO @ Sat, 03 Apr 2021 08:41:08: 10000000 INFO @ Sat, 03 Apr 2021 08:41:11: 18000000 INFO @ Sat, 03 Apr 2021 08:41:14: 14000000 INFO @ Sat, 03 Apr 2021 08:41:16: 11000000 INFO @ Sat, 03 Apr 2021 08:41:19: 19000000 INFO @ Sat, 03 Apr 2021 08:41:22: 15000000 INFO @ Sat, 03 Apr 2021 08:41:24: 12000000 INFO @ Sat, 03 Apr 2021 08:41:27: 20000000 INFO @ Sat, 03 Apr 2021 08:41:30: 16000000 INFO @ Sat, 03 Apr 2021 08:41:32: 13000000 INFO @ Sat, 03 Apr 2021 08:41:35: 21000000 INFO @ Sat, 03 Apr 2021 08:41:38: 17000000 INFO @ Sat, 03 Apr 2021 08:41:39: 14000000 INFO @ Sat, 03 Apr 2021 08:41:43: 22000000 INFO @ Sat, 03 Apr 2021 08:41:46: 18000000 INFO @ Sat, 03 Apr 2021 08:41:47: 15000000 INFO @ Sat, 03 Apr 2021 08:41:51: 23000000 INFO @ Sat, 03 Apr 2021 08:41:53: 19000000 INFO @ Sat, 03 Apr 2021 08:41:55: 16000000 INFO @ Sat, 03 Apr 2021 08:41:58: 24000000 INFO @ Sat, 03 Apr 2021 08:42:01: 20000000 INFO @ Sat, 03 Apr 2021 08:42:02: 17000000 INFO @ Sat, 03 Apr 2021 08:42:06: 25000000 INFO @ Sat, 03 Apr 2021 08:42:09: 21000000 INFO @ Sat, 03 Apr 2021 08:42:10: 18000000 INFO @ Sat, 03 Apr 2021 08:42:14: 26000000 INFO @ Sat, 03 Apr 2021 08:42:17: 22000000 INFO @ Sat, 03 Apr 2021 08:42:18: 19000000 INFO @ Sat, 03 Apr 2021 08:42:22: 27000000 INFO @ Sat, 03 Apr 2021 08:42:24: 23000000 INFO @ Sat, 03 Apr 2021 08:42:26: 20000000 INFO @ Sat, 03 Apr 2021 08:42:29: 28000000 INFO @ Sat, 03 Apr 2021 08:42:32: 24000000 INFO @ Sat, 03 Apr 2021 08:42:33: 21000000 INFO @ Sat, 03 Apr 2021 08:42:37: 29000000 INFO @ Sat, 03 Apr 2021 08:42:39: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:42:41: 22000000 INFO @ Sat, 03 Apr 2021 08:42:45: 30000000 INFO @ Sat, 03 Apr 2021 08:42:47: 26000000 INFO @ Sat, 03 Apr 2021 08:42:48: 23000000 INFO @ Sat, 03 Apr 2021 08:42:53: 31000000 INFO @ Sat, 03 Apr 2021 08:42:55: 27000000 INFO @ Sat, 03 Apr 2021 08:42:56: 24000000 INFO @ Sat, 03 Apr 2021 08:43:01: 32000000 INFO @ Sat, 03 Apr 2021 08:43:03: 28000000 INFO @ Sat, 03 Apr 2021 08:43:03: 25000000 INFO @ Sat, 03 Apr 2021 08:43:06: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:43:06: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:43:06: #1 total tags in treatment: 12389193 INFO @ Sat, 03 Apr 2021 08:43:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:43:06: #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 08:43:06: #1 tags after filtering in treatment: 9811836 INFO @ Sat, 03 Apr 2021 08:43:06: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:43:06: #1 finished! INFO @ Sat, 03 Apr 2021 08:43:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:43:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:43:07: #2 number of paired peaks: 353 WARNING @ Sat, 03 Apr 2021 08:43:07: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Sat, 03 Apr 2021 08:43:07: start model_add_line... INFO @ Sat, 03 Apr 2021 08:43:07: start X-correlation... INFO @ Sat, 03 Apr 2021 08:43:07: end of X-cor INFO @ Sat, 03 Apr 2021 08:43:07: #2 finished! INFO @ Sat, 03 Apr 2021 08:43:07: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 08:43:07: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 03 Apr 2021 08:43:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.05_model.r WARNING @ Sat, 03 Apr 2021 08:43:07: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:43:07: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sat, 03 Apr 2021 08:43:07: #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 08:43:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:43:10: 26000000 INFO @ Sat, 03 Apr 2021 08:43:10: 29000000 INFO @ Sat, 03 Apr 2021 08:43:18: 27000000 INFO @ Sat, 03 Apr 2021 08:43:18: 30000000 INFO @ Sat, 03 Apr 2021 08:43:26: 28000000 INFO @ Sat, 03 Apr 2021 08:43:26: 31000000 INFO @ Sat, 03 Apr 2021 08:43:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:43:33: 29000000 INFO @ Sat, 03 Apr 2021 08:43:33: 32000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:43:39: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:43:39: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:43:39: #1 total tags in treatment: 12389193 INFO @ Sat, 03 Apr 2021 08:43:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:43:39: #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 08:43:39: #1 tags after filtering in treatment: 9811836 INFO @ Sat, 03 Apr 2021 08:43:39: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:43:39: #1 finished! INFO @ Sat, 03 Apr 2021 08:43:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:43:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:43:40: #2 number of paired peaks: 353 WARNING @ Sat, 03 Apr 2021 08:43:40: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Sat, 03 Apr 2021 08:43:40: start model_add_line... INFO @ Sat, 03 Apr 2021 08:43:40: start X-correlation... INFO @ Sat, 03 Apr 2021 08:43:40: end of X-cor INFO @ Sat, 03 Apr 2021 08:43:40: #2 finished! INFO @ Sat, 03 Apr 2021 08:43:40: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 08:43:40: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 03 Apr 2021 08:43:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.10_model.r WARNING @ Sat, 03 Apr 2021 08:43:40: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:43:40: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sat, 03 Apr 2021 08:43:40: #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 08:43:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:43:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:43:41: 30000000 INFO @ Sat, 03 Apr 2021 08:43:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:43:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:43:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.05_summits.bed INFO @ Sat, 03 Apr 2021 08:43:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6797 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:43:48: 31000000 INFO @ Sat, 03 Apr 2021 08:43:55: 32000000 INFO @ Sat, 03 Apr 2021 08:44:00: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:44:00: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:44:00: #1 total tags in treatment: 12389193 INFO @ Sat, 03 Apr 2021 08:44:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:44:00: #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 08:44:00: #1 tags after filtering in treatment: 9811836 INFO @ Sat, 03 Apr 2021 08:44:00: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:44:00: #1 finished! INFO @ Sat, 03 Apr 2021 08:44:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:44:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:44:01: #2 number of paired peaks: 353 WARNING @ Sat, 03 Apr 2021 08:44:01: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Sat, 03 Apr 2021 08:44:01: start model_add_line... INFO @ Sat, 03 Apr 2021 08:44:01: start X-correlation... INFO @ Sat, 03 Apr 2021 08:44:01: end of X-cor INFO @ Sat, 03 Apr 2021 08:44:01: #2 finished! INFO @ Sat, 03 Apr 2021 08:44:01: #2 predicted fragment length is 89 bps INFO @ Sat, 03 Apr 2021 08:44:01: #2 alternative fragment length(s) may be 4,89 bps INFO @ Sat, 03 Apr 2021 08:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.20_model.r WARNING @ Sat, 03 Apr 2021 08:44:01: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:44:01: #2 You may need to consider one of the other alternative d(s): 4,89 WARNING @ Sat, 03 Apr 2021 08:44:01: #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 08:44:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.10_summits.bed INFO @ Sat, 03 Apr 2021 08:44:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1701 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:44:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277035/SRX7277035.20_summits.bed INFO @ Sat, 03 Apr 2021 08:44:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling