Job ID = 6626503 SRX = SRX5736481 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11680530 spots for SRR8956892/SRR8956892.sra Written 11680530 spots for SRR8956892/SRR8956892.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626698 ("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: 00:30:10 11680530 reads; of these: 11680530 (100.00%) were paired; of these: 1869727 (16.01%) aligned concordantly 0 times 6339552 (54.27%) aligned concordantly exactly 1 time 3471251 (29.72%) aligned concordantly >1 times ---- 1869727 pairs aligned concordantly 0 times; of these: 277863 (14.86%) aligned discordantly 1 time ---- 1591864 pairs aligned 0 times concordantly or discordantly; of these: 3183728 mates make up the pairs; of these: 2444617 (76.78%) aligned 0 times 324884 (10.20%) aligned exactly 1 time 414227 (13.01%) aligned >1 times 89.54% overall alignment rate Time searching: 00:30:10 Overall time: 00:30:10 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 12 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] 851818 / 10020871 = 0.0850 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.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 @ Tue, 14 Jul 2020 07:46:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:46:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:46:17: 1000000 INFO @ Tue, 14 Jul 2020 07:46:23: 2000000 INFO @ Tue, 14 Jul 2020 07:46:28: 3000000 INFO @ Tue, 14 Jul 2020 07:46:34: 4000000 INFO @ Tue, 14 Jul 2020 07:46:39: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.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 @ Tue, 14 Jul 2020 07:46:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:46:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:46:45: 6000000 INFO @ Tue, 14 Jul 2020 07:46:48: 1000000 INFO @ Tue, 14 Jul 2020 07:46:52: 7000000 INFO @ Tue, 14 Jul 2020 07:46:55: 2000000 INFO @ Tue, 14 Jul 2020 07:46:59: 8000000 INFO @ Tue, 14 Jul 2020 07:47:01: 3000000 INFO @ Tue, 14 Jul 2020 07:47:05: 9000000 INFO @ Tue, 14 Jul 2020 07:47:08: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:47:12: 10000000 INFO @ Tue, 14 Jul 2020 07:47:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.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 @ Tue, 14 Jul 2020 07:47:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:47:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:47:14: 5000000 INFO @ Tue, 14 Jul 2020 07:47:18: 11000000 INFO @ Tue, 14 Jul 2020 07:47:18: 1000000 INFO @ Tue, 14 Jul 2020 07:47:21: 6000000 INFO @ Tue, 14 Jul 2020 07:47:25: 12000000 INFO @ Tue, 14 Jul 2020 07:47:25: 2000000 INFO @ Tue, 14 Jul 2020 07:47:27: 7000000 INFO @ Tue, 14 Jul 2020 07:47:31: 13000000 INFO @ Tue, 14 Jul 2020 07:47:32: 3000000 INFO @ Tue, 14 Jul 2020 07:47:34: 8000000 INFO @ Tue, 14 Jul 2020 07:47:38: 14000000 INFO @ Tue, 14 Jul 2020 07:47:38: 4000000 INFO @ Tue, 14 Jul 2020 07:47:41: 9000000 INFO @ Tue, 14 Jul 2020 07:47:45: 15000000 INFO @ Tue, 14 Jul 2020 07:47:45: 5000000 INFO @ Tue, 14 Jul 2020 07:47:47: 10000000 INFO @ Tue, 14 Jul 2020 07:47:51: 16000000 INFO @ Tue, 14 Jul 2020 07:47:52: 6000000 INFO @ Tue, 14 Jul 2020 07:47:54: 11000000 INFO @ Tue, 14 Jul 2020 07:47:58: 17000000 INFO @ Tue, 14 Jul 2020 07:47:58: 7000000 INFO @ Tue, 14 Jul 2020 07:48:00: 12000000 INFO @ Tue, 14 Jul 2020 07:48:05: 18000000 INFO @ Tue, 14 Jul 2020 07:48:05: 8000000 INFO @ Tue, 14 Jul 2020 07:48:07: 13000000 INFO @ Tue, 14 Jul 2020 07:48:11: 19000000 INFO @ Tue, 14 Jul 2020 07:48:12: 9000000 INFO @ Tue, 14 Jul 2020 07:48:13: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:48:13: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:48:13: #1 total tags in treatment: 8969520 INFO @ Tue, 14 Jul 2020 07:48:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:48:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:48:13: #1 tags after filtering in treatment: 8224320 INFO @ Tue, 14 Jul 2020 07:48:13: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:48:13: #1 finished! INFO @ Tue, 14 Jul 2020 07:48:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:48:13: #2 number of paired peaks: 184 WARNING @ Tue, 14 Jul 2020 07:48:13: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 14 Jul 2020 07:48:13: start model_add_line... INFO @ Tue, 14 Jul 2020 07:48:13: start X-correlation... INFO @ Tue, 14 Jul 2020 07:48:13: end of X-cor INFO @ Tue, 14 Jul 2020 07:48:13: #2 finished! INFO @ Tue, 14 Jul 2020 07:48:13: #2 predicted fragment length is 131 bps INFO @ Tue, 14 Jul 2020 07:48:13: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 14 Jul 2020 07:48:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.05_model.r WARNING @ Tue, 14 Jul 2020 07:48:13: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:48:13: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Tue, 14 Jul 2020 07:48:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:48:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:48:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:48:13: 14000000 INFO @ Tue, 14 Jul 2020 07:48:18: 10000000 INFO @ Tue, 14 Jul 2020 07:48:20: 15000000 INFO @ Tue, 14 Jul 2020 07:48:25: 11000000 INFO @ Tue, 14 Jul 2020 07:48:27: 16000000 INFO @ Tue, 14 Jul 2020 07:48:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:48:31: 12000000 INFO @ Tue, 14 Jul 2020 07:48:33: 17000000 INFO @ Tue, 14 Jul 2020 07:48:38: 13000000 INFO @ Tue, 14 Jul 2020 07:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.05_summits.bed INFO @ Tue, 14 Jul 2020 07:48:39: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1613 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:48:40: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:48:45: 14000000 INFO @ Tue, 14 Jul 2020 07:48:46: 19000000 INFO @ Tue, 14 Jul 2020 07:48:48: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:48:48: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:48:48: #1 total tags in treatment: 8969520 INFO @ Tue, 14 Jul 2020 07:48:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:48:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:48:48: #1 tags after filtering in treatment: 8224320 INFO @ Tue, 14 Jul 2020 07:48:48: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:48:48: #1 finished! INFO @ Tue, 14 Jul 2020 07:48:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:48:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:48:48: #2 number of paired peaks: 184 WARNING @ Tue, 14 Jul 2020 07:48:48: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 14 Jul 2020 07:48:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:48:48: start X-correlation... INFO @ Tue, 14 Jul 2020 07:48:48: end of X-cor INFO @ Tue, 14 Jul 2020 07:48:48: #2 finished! INFO @ Tue, 14 Jul 2020 07:48:48: #2 predicted fragment length is 131 bps INFO @ Tue, 14 Jul 2020 07:48:48: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 14 Jul 2020 07:48:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.10_model.r WARNING @ Tue, 14 Jul 2020 07:48:48: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:48:48: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Tue, 14 Jul 2020 07:48:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:48:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:48:51: 15000000 INFO @ Tue, 14 Jul 2020 07:48:57: 16000000 INFO @ Tue, 14 Jul 2020 07:49:03: 17000000 INFO @ Tue, 14 Jul 2020 07:49:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:09: 18000000 INFO @ Tue, 14 Jul 2020 07:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.10_summits.bed INFO @ Tue, 14 Jul 2020 07:49:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (941 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:49:15: 19000000 INFO @ Tue, 14 Jul 2020 07:49:17: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:49:17: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:49:17: #1 total tags in treatment: 8969520 INFO @ Tue, 14 Jul 2020 07:49:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:49:17: #1 tags after filtering in treatment: 8224320 INFO @ Tue, 14 Jul 2020 07:49:17: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 14 Jul 2020 07:49:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:49:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:49:17: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:49:17: #2 number of paired peaks: 184 WARNING @ Tue, 14 Jul 2020 07:49:17: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 14 Jul 2020 07:49:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:49:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:49:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:49:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:49:18: #2 predicted fragment length is 131 bps INFO @ Tue, 14 Jul 2020 07:49:18: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 14 Jul 2020 07:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.20_model.r WARNING @ Tue, 14 Jul 2020 07:49:18: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:49:18: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Tue, 14 Jul 2020 07:49:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:49:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:49:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:49:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:49:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:49:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736481/SRX5736481.20_summits.bed INFO @ Tue, 14 Jul 2020 07:49:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 15 millis CompletedMACS2peakCalling