Job ID = 12265577 SRX = SRX7277031 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26402734 spots for SRR10597296/SRR10597296.sra Written 26402734 spots for SRR10597296/SRR10597296.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265922 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:45:17 26402734 reads; of these: 26402734 (100.00%) were paired; of these: 10039930 (38.03%) aligned concordantly 0 times 10605093 (40.17%) aligned concordantly exactly 1 time 5757711 (21.81%) aligned concordantly >1 times ---- 10039930 pairs aligned concordantly 0 times; of these: 2585368 (25.75%) aligned discordantly 1 time ---- 7454562 pairs aligned 0 times concordantly or discordantly; of these: 14909124 mates make up the pairs; of these: 11745136 (78.78%) aligned 0 times 744358 (4.99%) aligned exactly 1 time 2419630 (16.23%) aligned >1 times 77.76% overall alignment rate Time searching: 00:45:18 Overall time: 00:45:18 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] 3646560 / 18798361 = 0.1940 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 08:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.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 08:43:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:43:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:43:50: 1000000 INFO @ Sat, 03 Apr 2021 08:43:56: 2000000 INFO @ Sat, 03 Apr 2021 08:44:01: 3000000 INFO @ Sat, 03 Apr 2021 08:44:07: 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 08:44:13: 5000000 INFO @ Sat, 03 Apr 2021 08:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.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 08:44:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:44:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:44:18: 6000000 INFO @ Sat, 03 Apr 2021 08:44:20: 1000000 INFO @ Sat, 03 Apr 2021 08:44:24: 7000000 INFO @ Sat, 03 Apr 2021 08:44:26: 2000000 INFO @ Sat, 03 Apr 2021 08:44:30: 8000000 INFO @ Sat, 03 Apr 2021 08:44:32: 3000000 INFO @ Sat, 03 Apr 2021 08:44:36: 9000000 INFO @ Sat, 03 Apr 2021 08:44:37: 4000000 INFO @ Sat, 03 Apr 2021 08:44:41: 10000000 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 08:44:43: 5000000 INFO @ Sat, 03 Apr 2021 08:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.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 08:44:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:44:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:44:47: 11000000 INFO @ Sat, 03 Apr 2021 08:44:48: 6000000 INFO @ Sat, 03 Apr 2021 08:44:51: 1000000 INFO @ Sat, 03 Apr 2021 08:44:54: 12000000 INFO @ Sat, 03 Apr 2021 08:44:54: 7000000 INFO @ Sat, 03 Apr 2021 08:44:57: 2000000 INFO @ Sat, 03 Apr 2021 08:44:59: 8000000 INFO @ Sat, 03 Apr 2021 08:45:00: 13000000 INFO @ Sat, 03 Apr 2021 08:45:04: 3000000 INFO @ Sat, 03 Apr 2021 08:45:05: 9000000 INFO @ Sat, 03 Apr 2021 08:45:06: 14000000 INFO @ Sat, 03 Apr 2021 08:45:10: 4000000 INFO @ Sat, 03 Apr 2021 08:45:11: 10000000 INFO @ Sat, 03 Apr 2021 08:45:13: 15000000 INFO @ Sat, 03 Apr 2021 08:45:16: 11000000 INFO @ Sat, 03 Apr 2021 08:45:17: 5000000 INFO @ Sat, 03 Apr 2021 08:45:19: 16000000 INFO @ Sat, 03 Apr 2021 08:45:22: 12000000 INFO @ Sat, 03 Apr 2021 08:45:23: 6000000 INFO @ Sat, 03 Apr 2021 08:45:25: 17000000 INFO @ Sat, 03 Apr 2021 08:45:27: 13000000 INFO @ Sat, 03 Apr 2021 08:45:29: 7000000 INFO @ Sat, 03 Apr 2021 08:45:32: 18000000 INFO @ Sat, 03 Apr 2021 08:45:33: 14000000 INFO @ Sat, 03 Apr 2021 08:45:36: 8000000 INFO @ Sat, 03 Apr 2021 08:45:38: 19000000 INFO @ Sat, 03 Apr 2021 08:45:39: 15000000 INFO @ Sat, 03 Apr 2021 08:45:42: 9000000 INFO @ Sat, 03 Apr 2021 08:45:44: 20000000 INFO @ Sat, 03 Apr 2021 08:45:44: 16000000 INFO @ Sat, 03 Apr 2021 08:45:48: 10000000 INFO @ Sat, 03 Apr 2021 08:45:50: 17000000 INFO @ Sat, 03 Apr 2021 08:45:50: 21000000 INFO @ Sat, 03 Apr 2021 08:45:54: 11000000 INFO @ Sat, 03 Apr 2021 08:45:55: 18000000 INFO @ Sat, 03 Apr 2021 08:45:57: 22000000 INFO @ Sat, 03 Apr 2021 08:46:01: 12000000 INFO @ Sat, 03 Apr 2021 08:46:02: 19000000 INFO @ Sat, 03 Apr 2021 08:46:03: 23000000 INFO @ Sat, 03 Apr 2021 08:46:07: 13000000 INFO @ Sat, 03 Apr 2021 08:46:07: 20000000 INFO @ Sat, 03 Apr 2021 08:46:09: 24000000 INFO @ Sat, 03 Apr 2021 08:46:13: 21000000 INFO @ Sat, 03 Apr 2021 08:46:13: 14000000 INFO @ Sat, 03 Apr 2021 08:46:15: 25000000 INFO @ Sat, 03 Apr 2021 08:46:18: 22000000 INFO @ Sat, 03 Apr 2021 08:46:20: 15000000 INFO @ Sat, 03 Apr 2021 08:46:21: 26000000 INFO @ Sat, 03 Apr 2021 08:46:24: 23000000 INFO @ Sat, 03 Apr 2021 08:46:25: 16000000 INFO @ Sat, 03 Apr 2021 08:46:27: 27000000 INFO @ Sat, 03 Apr 2021 08:46:29: 24000000 INFO @ Sat, 03 Apr 2021 08:46:32: 17000000 INFO @ Sat, 03 Apr 2021 08:46:33: 28000000 INFO @ Sat, 03 Apr 2021 08:46:34: 25000000 INFO @ Sat, 03 Apr 2021 08:46:38: 18000000 INFO @ Sat, 03 Apr 2021 08:46:39: 29000000 INFO @ Sat, 03 Apr 2021 08:46:39: 26000000 INFO @ Sat, 03 Apr 2021 08:46:44: 19000000 INFO @ Sat, 03 Apr 2021 08:46:45: 27000000 INFO @ Sat, 03 Apr 2021 08:46:45: 30000000 INFO @ Sat, 03 Apr 2021 08:46:50: 20000000 INFO @ Sat, 03 Apr 2021 08:46:50: 28000000 INFO @ Sat, 03 Apr 2021 08:46:52: 31000000 INFO @ Sat, 03 Apr 2021 08:46:56: 29000000 INFO @ Sat, 03 Apr 2021 08:46:56: 21000000 INFO @ Sat, 03 Apr 2021 08:46:58: 32000000 INFO @ Sat, 03 Apr 2021 08:47:01: 30000000 INFO @ Sat, 03 Apr 2021 08:47:03: 22000000 INFO @ Sat, 03 Apr 2021 08:47:04: 33000000 INFO @ Sat, 03 Apr 2021 08:47:07: 31000000 INFO @ Sat, 03 Apr 2021 08:47:09: 23000000 INFO @ Sat, 03 Apr 2021 08:47:09: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:47:09: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:47:09: #1 total tags in treatment: 12844044 INFO @ Sat, 03 Apr 2021 08:47:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:47:09: #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 08:47:10: #1 tags after filtering in treatment: 10014395 INFO @ Sat, 03 Apr 2021 08:47:10: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 08:47:10: #1 finished! INFO @ Sat, 03 Apr 2021 08:47:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:47:10: #2 number of paired peaks: 428 WARNING @ Sat, 03 Apr 2021 08:47:10: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sat, 03 Apr 2021 08:47:10: start model_add_line... INFO @ Sat, 03 Apr 2021 08:47:11: start X-correlation... INFO @ Sat, 03 Apr 2021 08:47:11: end of X-cor INFO @ Sat, 03 Apr 2021 08:47:11: #2 finished! INFO @ Sat, 03 Apr 2021 08:47:11: #2 predicted fragment length is 75 bps INFO @ Sat, 03 Apr 2021 08:47:11: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sat, 03 Apr 2021 08:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.05_model.r WARNING @ Sat, 03 Apr 2021 08:47:11: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:47:11: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sat, 03 Apr 2021 08:47:11: #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 08:47:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:47:13: 32000000 INFO @ Sat, 03 Apr 2021 08:47:14: 24000000 INFO @ Sat, 03 Apr 2021 08:47:19: 33000000 INFO @ Sat, 03 Apr 2021 08:47:19: 25000000 INFO @ Sat, 03 Apr 2021 08:47:23: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:47:23: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:47:23: #1 total tags in treatment: 12844044 INFO @ Sat, 03 Apr 2021 08:47:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:47:23: #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 08:47:23: #1 tags after filtering in treatment: 10014395 INFO @ Sat, 03 Apr 2021 08:47:23: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 08:47:23: #1 finished! INFO @ Sat, 03 Apr 2021 08:47:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:47:24: #2 number of paired peaks: 428 WARNING @ Sat, 03 Apr 2021 08:47:24: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sat, 03 Apr 2021 08:47:24: start model_add_line... INFO @ Sat, 03 Apr 2021 08:47:24: start X-correlation... INFO @ Sat, 03 Apr 2021 08:47:24: end of X-cor INFO @ Sat, 03 Apr 2021 08:47:24: #2 finished! INFO @ Sat, 03 Apr 2021 08:47:24: #2 predicted fragment length is 75 bps INFO @ Sat, 03 Apr 2021 08:47:24: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sat, 03 Apr 2021 08:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.10_model.r WARNING @ Sat, 03 Apr 2021 08:47:24: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:47:24: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sat, 03 Apr 2021 08:47:24: #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 08:47:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:47:24: 26000000 INFO @ Sat, 03 Apr 2021 08:47:30: 27000000 INFO @ Sat, 03 Apr 2021 08:47:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:47:35: 28000000 INFO @ Sat, 03 Apr 2021 08:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.05_summits.bed INFO @ Sat, 03 Apr 2021 08:47:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7369 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:47:41: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:47:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:47:46: 30000000 INFO @ Sat, 03 Apr 2021 08:47:52: 31000000 INFO @ Sat, 03 Apr 2021 08:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.10_summits.bed INFO @ Sat, 03 Apr 2021 08:47:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1612 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:47:57: 32000000 INFO @ Sat, 03 Apr 2021 08:48:03: 33000000 INFO @ Sat, 03 Apr 2021 08:48:07: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:48:07: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:48:07: #1 total tags in treatment: 12844044 INFO @ Sat, 03 Apr 2021 08:48:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:48:07: #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 08:48:08: #1 tags after filtering in treatment: 10014395 INFO @ Sat, 03 Apr 2021 08:48:08: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 08:48:08: #1 finished! INFO @ Sat, 03 Apr 2021 08:48:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:48:08: #2 number of paired peaks: 428 WARNING @ Sat, 03 Apr 2021 08:48:08: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Sat, 03 Apr 2021 08:48:08: start model_add_line... INFO @ Sat, 03 Apr 2021 08:48:09: start X-correlation... INFO @ Sat, 03 Apr 2021 08:48:09: end of X-cor INFO @ Sat, 03 Apr 2021 08:48:09: #2 finished! INFO @ Sat, 03 Apr 2021 08:48:09: #2 predicted fragment length is 75 bps INFO @ Sat, 03 Apr 2021 08:48:09: #2 alternative fragment length(s) may be 4,75 bps INFO @ Sat, 03 Apr 2021 08:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.20_model.r WARNING @ Sat, 03 Apr 2021 08:48:09: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:48:09: #2 You may need to consider one of the other alternative d(s): 4,75 WARNING @ Sat, 03 Apr 2021 08:48:09: #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 08:48:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:48:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277031/SRX7277031.20_summits.bed INFO @ Sat, 03 Apr 2021 08:48:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (121 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。