Job ID = 6626523 SRX = SRX5736497 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17185130 spots for SRR8956908/SRR8956908.sra Written 17185130 spots for SRR8956908/SRR8956908.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626808 ("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: 00:56:13 17185130 reads; of these: 17185130 (100.00%) were paired; of these: 2115597 (12.31%) aligned concordantly 0 times 9181971 (53.43%) aligned concordantly exactly 1 time 5887562 (34.26%) aligned concordantly >1 times ---- 2115597 pairs aligned concordantly 0 times; of these: 404653 (19.13%) aligned discordantly 1 time ---- 1710944 pairs aligned 0 times concordantly or discordantly; of these: 3421888 mates make up the pairs; of these: 2231043 (65.20%) aligned 0 times 459410 (13.43%) aligned exactly 1 time 731435 (21.38%) aligned >1 times 93.51% overall alignment rate Time searching: 00:56:13 Overall time: 00:56:13 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 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] 784382 / 15432459 = 0.0508 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 08:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.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 08:26:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:26:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:26:56: 1000000 INFO @ Tue, 14 Jul 2020 08:27:02: 2000000 INFO @ Tue, 14 Jul 2020 08:27:08: 3000000 INFO @ Tue, 14 Jul 2020 08:27:14: 4000000 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 08:27:19: 5000000 INFO @ Tue, 14 Jul 2020 08:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.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 08:27:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:27:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:27:26: 6000000 INFO @ Tue, 14 Jul 2020 08:27:27: 1000000 INFO @ Tue, 14 Jul 2020 08:27:32: 7000000 INFO @ Tue, 14 Jul 2020 08:27:33: 2000000 INFO @ Tue, 14 Jul 2020 08:27:39: 8000000 INFO @ Tue, 14 Jul 2020 08:27:40: 3000000 INFO @ Tue, 14 Jul 2020 08:27:45: 9000000 INFO @ Tue, 14 Jul 2020 08:27:46: 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 08:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.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 08:27:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:27:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:27:52: 10000000 INFO @ Tue, 14 Jul 2020 08:27:53: 5000000 INFO @ Tue, 14 Jul 2020 08:27:57: 1000000 INFO @ Tue, 14 Jul 2020 08:27:58: 11000000 INFO @ Tue, 14 Jul 2020 08:28:00: 6000000 INFO @ Tue, 14 Jul 2020 08:28:06: 2000000 INFO @ Tue, 14 Jul 2020 08:28:07: 12000000 INFO @ Tue, 14 Jul 2020 08:28:09: 7000000 INFO @ Tue, 14 Jul 2020 08:28:13: 3000000 INFO @ Tue, 14 Jul 2020 08:28:13: 13000000 INFO @ Tue, 14 Jul 2020 08:28:16: 8000000 INFO @ Tue, 14 Jul 2020 08:28:20: 4000000 INFO @ Tue, 14 Jul 2020 08:28:20: 14000000 INFO @ Tue, 14 Jul 2020 08:28:23: 9000000 INFO @ Tue, 14 Jul 2020 08:28:27: 5000000 INFO @ Tue, 14 Jul 2020 08:28:27: 15000000 INFO @ Tue, 14 Jul 2020 08:28:30: 10000000 INFO @ Tue, 14 Jul 2020 08:28:34: 6000000 INFO @ Tue, 14 Jul 2020 08:28:34: 16000000 INFO @ Tue, 14 Jul 2020 08:28:37: 11000000 INFO @ Tue, 14 Jul 2020 08:28:41: 7000000 INFO @ Tue, 14 Jul 2020 08:28:41: 17000000 INFO @ Tue, 14 Jul 2020 08:28:44: 12000000 INFO @ Tue, 14 Jul 2020 08:28:48: 8000000 INFO @ Tue, 14 Jul 2020 08:28:48: 18000000 INFO @ Tue, 14 Jul 2020 08:28:51: 13000000 INFO @ Tue, 14 Jul 2020 08:28:55: 9000000 INFO @ Tue, 14 Jul 2020 08:28:55: 19000000 INFO @ Tue, 14 Jul 2020 08:28:58: 14000000 INFO @ Tue, 14 Jul 2020 08:29:02: 10000000 INFO @ Tue, 14 Jul 2020 08:29:02: 20000000 INFO @ Tue, 14 Jul 2020 08:29:04: 15000000 INFO @ Tue, 14 Jul 2020 08:29:08: 11000000 INFO @ Tue, 14 Jul 2020 08:29:08: 21000000 INFO @ Tue, 14 Jul 2020 08:29:11: 16000000 INFO @ Tue, 14 Jul 2020 08:29:15: 12000000 INFO @ Tue, 14 Jul 2020 08:29:15: 22000000 INFO @ Tue, 14 Jul 2020 08:29:18: 17000000 INFO @ Tue, 14 Jul 2020 08:29:22: 13000000 INFO @ Tue, 14 Jul 2020 08:29:22: 23000000 INFO @ Tue, 14 Jul 2020 08:29:25: 18000000 INFO @ Tue, 14 Jul 2020 08:29:29: 24000000 INFO @ Tue, 14 Jul 2020 08:29:29: 14000000 INFO @ Tue, 14 Jul 2020 08:29:31: 19000000 INFO @ Tue, 14 Jul 2020 08:29:35: 25000000 INFO @ Tue, 14 Jul 2020 08:29:35: 15000000 INFO @ Tue, 14 Jul 2020 08:29:38: 20000000 INFO @ Tue, 14 Jul 2020 08:29:42: 26000000 INFO @ Tue, 14 Jul 2020 08:29:42: 16000000 INFO @ Tue, 14 Jul 2020 08:29:45: 21000000 INFO @ Tue, 14 Jul 2020 08:29:49: 27000000 INFO @ Tue, 14 Jul 2020 08:29:49: 17000000 INFO @ Tue, 14 Jul 2020 08:29:52: 22000000 INFO @ Tue, 14 Jul 2020 08:29:56: 18000000 INFO @ Tue, 14 Jul 2020 08:29:56: 28000000 INFO @ Tue, 14 Jul 2020 08:29:59: 23000000 INFO @ Tue, 14 Jul 2020 08:30:02: 19000000 INFO @ Tue, 14 Jul 2020 08:30:03: 29000000 INFO @ Tue, 14 Jul 2020 08:30:05: 24000000 INFO @ Tue, 14 Jul 2020 08:30:09: 20000000 INFO @ Tue, 14 Jul 2020 08:30:10: 30000000 INFO @ Tue, 14 Jul 2020 08:30:12: 25000000 INFO @ Tue, 14 Jul 2020 08:30:14: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:30:14: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:30:14: #1 total tags in treatment: 14293581 INFO @ Tue, 14 Jul 2020 08:30:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:30:14: #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 08:30:14: #1 tags after filtering in treatment: 12675805 INFO @ Tue, 14 Jul 2020 08:30:14: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 08:30:14: #1 finished! INFO @ Tue, 14 Jul 2020 08:30:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:30:14: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:30:15: #2 number of paired peaks: 172 WARNING @ Tue, 14 Jul 2020 08:30:15: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 14 Jul 2020 08:30:15: start model_add_line... INFO @ Tue, 14 Jul 2020 08:30:15: start X-correlation... INFO @ Tue, 14 Jul 2020 08:30:15: end of X-cor INFO @ Tue, 14 Jul 2020 08:30:15: #2 finished! INFO @ Tue, 14 Jul 2020 08:30:15: #2 predicted fragment length is 139 bps INFO @ Tue, 14 Jul 2020 08:30:15: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 14 Jul 2020 08:30:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.05_model.r WARNING @ Tue, 14 Jul 2020 08:30:15: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:30:15: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 14 Jul 2020 08:30:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:30:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:30:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:30:16: 21000000 INFO @ Tue, 14 Jul 2020 08:30:19: 26000000 INFO @ Tue, 14 Jul 2020 08:30:23: 22000000 INFO @ Tue, 14 Jul 2020 08:30:26: 27000000 INFO @ Tue, 14 Jul 2020 08:30:29: 23000000 INFO @ Tue, 14 Jul 2020 08:30:32: 28000000 INFO @ Tue, 14 Jul 2020 08:30:36: 24000000 INFO @ Tue, 14 Jul 2020 08:30:39: 29000000 INFO @ Tue, 14 Jul 2020 08:30:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:30:42: 25000000 INFO @ Tue, 14 Jul 2020 08:30:46: 30000000 INFO @ Tue, 14 Jul 2020 08:30:49: 26000000 INFO @ Tue, 14 Jul 2020 08:30:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:30:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:30:50: #1 total tags in treatment: 14293581 INFO @ Tue, 14 Jul 2020 08:30:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:30:50: #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 08:30:50: #1 tags after filtering in treatment: 12675805 INFO @ Tue, 14 Jul 2020 08:30:50: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 08:30:50: #1 finished! INFO @ Tue, 14 Jul 2020 08:30:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:30:51: #2 number of paired peaks: 172 WARNING @ Tue, 14 Jul 2020 08:30:51: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 14 Jul 2020 08:30:51: start model_add_line... INFO @ Tue, 14 Jul 2020 08:30:51: start X-correlation... INFO @ Tue, 14 Jul 2020 08:30:51: end of X-cor INFO @ Tue, 14 Jul 2020 08:30:51: #2 finished! INFO @ Tue, 14 Jul 2020 08:30:51: #2 predicted fragment length is 139 bps INFO @ Tue, 14 Jul 2020 08:30:51: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 14 Jul 2020 08:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.10_model.r WARNING @ Tue, 14 Jul 2020 08:30:51: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:30:51: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 14 Jul 2020 08:30:51: #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 08:30:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:30:55: 27000000 INFO @ Tue, 14 Jul 2020 08:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.05_summits.bed INFO @ Tue, 14 Jul 2020 08:30:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5639 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:31:02: 28000000 INFO @ Tue, 14 Jul 2020 08:31:08: 29000000 INFO @ Tue, 14 Jul 2020 08:31:14: 30000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:31:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:31:18: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:31:18: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:31:18: #1 total tags in treatment: 14293581 INFO @ Tue, 14 Jul 2020 08:31:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:31:18: #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 08:31:18: #1 tags after filtering in treatment: 12675805 INFO @ Tue, 14 Jul 2020 08:31:18: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 14 Jul 2020 08:31:18: #1 finished! INFO @ Tue, 14 Jul 2020 08:31:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:31:19: #2 number of paired peaks: 172 WARNING @ Tue, 14 Jul 2020 08:31:19: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Tue, 14 Jul 2020 08:31:19: start model_add_line... INFO @ Tue, 14 Jul 2020 08:31:19: start X-correlation... INFO @ Tue, 14 Jul 2020 08:31:19: end of X-cor INFO @ Tue, 14 Jul 2020 08:31:19: #2 finished! INFO @ Tue, 14 Jul 2020 08:31:19: #2 predicted fragment length is 139 bps INFO @ Tue, 14 Jul 2020 08:31:19: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 14 Jul 2020 08:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.20_model.r WARNING @ Tue, 14 Jul 2020 08:31:19: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:31:19: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 14 Jul 2020 08:31:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:31:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:31:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:31:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:31:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:31:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.10_summits.bed INFO @ Tue, 14 Jul 2020 08:31:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2449 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:31:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736497/SRX5736497.20_summits.bed INFO @ Tue, 14 Jul 2020 08:31:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 20 millis CompletedMACS2peakCalling