Job ID = 16439430 SRX = SRX11245086 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:09:10 prefetch.2.10.7: 1) Downloading 'SRR14932351'... 2022-08-02T06:09:10 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:09:53 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:09:53 prefetch.2.10.7: 1) 'SRR14932351' was downloaded successfully 2022-08-02T06:09:53 prefetch.2.10.7: 'SRR14932351' has 0 unresolved dependencies Read 21833010 spots for SRR14932351/SRR14932351.sra Written 21833010 spots for SRR14932351/SRR14932351.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439997 ("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: 01:17:13 21833010 reads; of these: 21833010 (100.00%) were paired; of these: 9986530 (45.74%) aligned concordantly 0 times 9303659 (42.61%) aligned concordantly exactly 1 time 2542821 (11.65%) aligned concordantly >1 times ---- 9986530 pairs aligned concordantly 0 times; of these: 1702295 (17.05%) aligned discordantly 1 time ---- 8284235 pairs aligned 0 times concordantly or discordantly; of these: 16568470 mates make up the pairs; of these: 15089414 (91.07%) aligned 0 times 497608 (3.00%) aligned exactly 1 time 981448 (5.92%) aligned >1 times 65.44% overall alignment rate Time searching: 01:17:13 Overall time: 01:17:13 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 24 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] 4484425 / 13497502 = 0.3322 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.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, 02 Aug 2022 16:42:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:42:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:42:49: 1000000 INFO @ Tue, 02 Aug 2022 16:43:03: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.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, 02 Aug 2022 16:43:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:43:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:43:15: 1000000 INFO @ Tue, 02 Aug 2022 16:43:17: 3000000 INFO @ Tue, 02 Aug 2022 16:43:25: 2000000 INFO @ Tue, 02 Aug 2022 16:43:32: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:43:34: 3000000 INFO @ Tue, 02 Aug 2022 16:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.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, 02 Aug 2022 16:43:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:43:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:43:44: 4000000 INFO @ Tue, 02 Aug 2022 16:43:47: 5000000 INFO @ Tue, 02 Aug 2022 16:43:51: 1000000 INFO @ Tue, 02 Aug 2022 16:43:54: 5000000 INFO @ Tue, 02 Aug 2022 16:44:01: 6000000 INFO @ Tue, 02 Aug 2022 16:44:03: 6000000 INFO @ Tue, 02 Aug 2022 16:44:06: 2000000 INFO @ Tue, 02 Aug 2022 16:44:14: 7000000 INFO @ Tue, 02 Aug 2022 16:44:16: 7000000 INFO @ Tue, 02 Aug 2022 16:44:21: 3000000 INFO @ Tue, 02 Aug 2022 16:44:24: 8000000 INFO @ Tue, 02 Aug 2022 16:44:31: 8000000 INFO @ Tue, 02 Aug 2022 16:44:35: 4000000 INFO @ Tue, 02 Aug 2022 16:44:39: 9000000 INFO @ Tue, 02 Aug 2022 16:44:45: 9000000 INFO @ Tue, 02 Aug 2022 16:44:48: 10000000 INFO @ Tue, 02 Aug 2022 16:44:50: 5000000 INFO @ Tue, 02 Aug 2022 16:44:59: 11000000 INFO @ Tue, 02 Aug 2022 16:44:59: 10000000 INFO @ Tue, 02 Aug 2022 16:45:04: 6000000 INFO @ Tue, 02 Aug 2022 16:45:09: 12000000 INFO @ Tue, 02 Aug 2022 16:45:14: 11000000 INFO @ Tue, 02 Aug 2022 16:45:19: 7000000 INFO @ Tue, 02 Aug 2022 16:45:19: 13000000 INFO @ Tue, 02 Aug 2022 16:45:29: 12000000 INFO @ Tue, 02 Aug 2022 16:45:30: 14000000 INFO @ Tue, 02 Aug 2022 16:45:34: 8000000 INFO @ Tue, 02 Aug 2022 16:45:40: 15000000 INFO @ Tue, 02 Aug 2022 16:45:43: 13000000 INFO @ Tue, 02 Aug 2022 16:45:49: 9000000 INFO @ Tue, 02 Aug 2022 16:45:51: 16000000 INFO @ Tue, 02 Aug 2022 16:45:58: 14000000 INFO @ Tue, 02 Aug 2022 16:46:02: 17000000 INFO @ Tue, 02 Aug 2022 16:46:03: 10000000 INFO @ Tue, 02 Aug 2022 16:46:13: 15000000 INFO @ Tue, 02 Aug 2022 16:46:13: 18000000 INFO @ Tue, 02 Aug 2022 16:46:18: 11000000 INFO @ Tue, 02 Aug 2022 16:46:24: 19000000 INFO @ Tue, 02 Aug 2022 16:46:27: 16000000 INFO @ Tue, 02 Aug 2022 16:46:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:46:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:46:30: #1 total tags in treatment: 7965141 INFO @ Tue, 02 Aug 2022 16:46:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:46:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:46:30: #1 tags after filtering in treatment: 7595354 INFO @ Tue, 02 Aug 2022 16:46:30: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 16:46:30: #1 finished! INFO @ Tue, 02 Aug 2022 16:46:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:46:31: #2 number of paired peaks: 260 WARNING @ Tue, 02 Aug 2022 16:46:31: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 02 Aug 2022 16:46:31: start model_add_line... INFO @ Tue, 02 Aug 2022 16:46:31: start X-correlation... INFO @ Tue, 02 Aug 2022 16:46:31: end of X-cor INFO @ Tue, 02 Aug 2022 16:46:31: #2 finished! INFO @ Tue, 02 Aug 2022 16:46:31: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 16:46:31: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 16:46:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.10_model.r WARNING @ Tue, 02 Aug 2022 16:46:31: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:46:31: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Tue, 02 Aug 2022 16:46:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:46:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:46:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:46:33: 12000000 INFO @ Tue, 02 Aug 2022 16:46:42: 17000000 INFO @ Tue, 02 Aug 2022 16:46:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:46:48: 13000000 INFO @ Tue, 02 Aug 2022 16:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:46:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:46:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.10_summits.bed INFO @ Tue, 02 Aug 2022 16:46:54: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (828 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:46:56: 18000000 INFO @ Tue, 02 Aug 2022 16:47:01: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:47:10: 19000000 INFO @ Tue, 02 Aug 2022 16:47:14: 15000000 INFO @ Tue, 02 Aug 2022 16:47:18: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:47:18: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:47:18: #1 total tags in treatment: 7965141 INFO @ Tue, 02 Aug 2022 16:47:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:47:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:47:18: #1 tags after filtering in treatment: 7595354 INFO @ Tue, 02 Aug 2022 16:47:18: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 16:47:18: #1 finished! INFO @ Tue, 02 Aug 2022 16:47:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:47:19: #2 number of paired peaks: 260 WARNING @ Tue, 02 Aug 2022 16:47:19: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 02 Aug 2022 16:47:19: start model_add_line... INFO @ Tue, 02 Aug 2022 16:47:19: start X-correlation... INFO @ Tue, 02 Aug 2022 16:47:19: end of X-cor INFO @ Tue, 02 Aug 2022 16:47:19: #2 finished! INFO @ Tue, 02 Aug 2022 16:47:19: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 16:47:19: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 16:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.05_model.r WARNING @ Tue, 02 Aug 2022 16:47:19: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:47:19: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Tue, 02 Aug 2022 16:47:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:47:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:47:28: 16000000 INFO @ Tue, 02 Aug 2022 16:47:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:47:42: 17000000 INFO @ Tue, 02 Aug 2022 16:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.05_summits.bed INFO @ Tue, 02 Aug 2022 16:47:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1296 records, 4 fields): 156 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:47:55: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:48:07: 19000000 INFO @ Tue, 02 Aug 2022 16:48:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 16:48:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 16:48:14: #1 total tags in treatment: 7965141 INFO @ Tue, 02 Aug 2022 16:48:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:48:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:48:14: #1 tags after filtering in treatment: 7595354 INFO @ Tue, 02 Aug 2022 16:48:14: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 16:48:14: #1 finished! INFO @ Tue, 02 Aug 2022 16:48:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:48:15: #2 number of paired peaks: 260 WARNING @ Tue, 02 Aug 2022 16:48:15: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Tue, 02 Aug 2022 16:48:15: start model_add_line... INFO @ Tue, 02 Aug 2022 16:48:15: start X-correlation... INFO @ Tue, 02 Aug 2022 16:48:15: end of X-cor INFO @ Tue, 02 Aug 2022 16:48:15: #2 finished! INFO @ Tue, 02 Aug 2022 16:48:15: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 16:48:15: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 16:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.20_model.r WARNING @ Tue, 02 Aug 2022 16:48:15: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:48:15: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Tue, 02 Aug 2022 16:48:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:48:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:48:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245086/SRX11245086.20_summits.bed INFO @ Tue, 02 Aug 2022 16:48:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (523 records, 4 fields): 53 millis CompletedMACS2peakCalling