Job ID = 16436397 SRX = SRX12440708 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35625369 spots for SRR16155889/SRR16155889.sra Written 35625369 spots for SRR16155889/SRR16155889.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438020 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:32:42 35625369 reads; of these: 35625369 (100.00%) were paired; of these: 26082847 (73.21%) aligned concordantly 0 times 8490906 (23.83%) aligned concordantly exactly 1 time 1051616 (2.95%) aligned concordantly >1 times ---- 26082847 pairs aligned concordantly 0 times; of these: 2825217 (10.83%) aligned discordantly 1 time ---- 23257630 pairs aligned 0 times concordantly or discordantly; of these: 46515260 mates make up the pairs; of these: 45167876 (97.10%) aligned 0 times 672073 (1.44%) aligned exactly 1 time 675311 (1.45%) aligned >1 times 36.61% overall alignment rate Time searching: 01:32:43 Overall time: 01:32:43 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] 2561251 / 12309132 = 0.2081 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 13:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.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 13:24:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:24:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:24:36: 1000000 INFO @ Tue, 02 Aug 2022 13:24:47: 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 13:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.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 13:24:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:24:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:24:58: 3000000 INFO @ Tue, 02 Aug 2022 13:25:05: 1000000 INFO @ Tue, 02 Aug 2022 13:25:09: 4000000 INFO @ Tue, 02 Aug 2022 13:25:16: 2000000 INFO @ Tue, 02 Aug 2022 13:25:20: 5000000 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 13:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.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 13:25:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:25:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:25:27: 3000000 INFO @ Tue, 02 Aug 2022 13:25:31: 6000000 INFO @ Tue, 02 Aug 2022 13:25:35: 1000000 INFO @ Tue, 02 Aug 2022 13:25:38: 4000000 INFO @ Tue, 02 Aug 2022 13:25:43: 7000000 INFO @ Tue, 02 Aug 2022 13:25:46: 2000000 INFO @ Tue, 02 Aug 2022 13:25:49: 5000000 INFO @ Tue, 02 Aug 2022 13:25:55: 8000000 INFO @ Tue, 02 Aug 2022 13:25:58: 3000000 INFO @ Tue, 02 Aug 2022 13:26:00: 6000000 INFO @ Tue, 02 Aug 2022 13:26:06: 9000000 INFO @ Tue, 02 Aug 2022 13:26:09: 4000000 INFO @ Tue, 02 Aug 2022 13:26:11: 7000000 INFO @ Tue, 02 Aug 2022 13:26:18: 10000000 INFO @ Tue, 02 Aug 2022 13:26:20: 5000000 INFO @ Tue, 02 Aug 2022 13:26:23: 8000000 INFO @ Tue, 02 Aug 2022 13:26:29: 11000000 INFO @ Tue, 02 Aug 2022 13:26:31: 6000000 INFO @ Tue, 02 Aug 2022 13:26:34: 9000000 INFO @ Tue, 02 Aug 2022 13:26:40: 12000000 INFO @ Tue, 02 Aug 2022 13:26:42: 7000000 INFO @ Tue, 02 Aug 2022 13:26:45: 10000000 INFO @ Tue, 02 Aug 2022 13:26:51: 13000000 INFO @ Tue, 02 Aug 2022 13:26:52: 8000000 INFO @ Tue, 02 Aug 2022 13:26:56: 11000000 INFO @ Tue, 02 Aug 2022 13:27:02: 14000000 INFO @ Tue, 02 Aug 2022 13:27:03: 9000000 INFO @ Tue, 02 Aug 2022 13:27:07: 12000000 INFO @ Tue, 02 Aug 2022 13:27:13: 15000000 INFO @ Tue, 02 Aug 2022 13:27:14: 10000000 INFO @ Tue, 02 Aug 2022 13:27:18: 13000000 INFO @ Tue, 02 Aug 2022 13:27:24: 16000000 INFO @ Tue, 02 Aug 2022 13:27:25: 11000000 INFO @ Tue, 02 Aug 2022 13:27:29: 14000000 INFO @ Tue, 02 Aug 2022 13:27:35: 17000000 INFO @ Tue, 02 Aug 2022 13:27:36: 12000000 INFO @ Tue, 02 Aug 2022 13:27:40: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:27:46: 18000000 INFO @ Tue, 02 Aug 2022 13:27:47: 13000000 INFO @ Tue, 02 Aug 2022 13:27:51: 16000000 INFO @ Tue, 02 Aug 2022 13:27:57: 19000000 INFO @ Tue, 02 Aug 2022 13:27:58: 14000000 INFO @ Tue, 02 Aug 2022 13:28:02: 17000000 INFO @ Tue, 02 Aug 2022 13:28:08: 20000000 INFO @ Tue, 02 Aug 2022 13:28:09: 15000000 INFO @ Tue, 02 Aug 2022 13:28:13: 18000000 INFO @ Tue, 02 Aug 2022 13:28:19: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:28:19: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:28:19: #1 total tags in treatment: 7577217 INFO @ Tue, 02 Aug 2022 13:28:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:28:19: #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 13:28:19: #1 tags after filtering in treatment: 5529108 INFO @ Tue, 02 Aug 2022 13:28:19: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 13:28:19: #1 finished! INFO @ Tue, 02 Aug 2022 13:28:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:28:20: 16000000 INFO @ Tue, 02 Aug 2022 13:28:20: #2 number of paired peaks: 5871 INFO @ Tue, 02 Aug 2022 13:28:20: start model_add_line... INFO @ Tue, 02 Aug 2022 13:28:20: start X-correlation... INFO @ Tue, 02 Aug 2022 13:28:20: end of X-cor INFO @ Tue, 02 Aug 2022 13:28:20: #2 finished! INFO @ Tue, 02 Aug 2022 13:28:20: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:28:20: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.05_model.r WARNING @ Tue, 02 Aug 2022 13:28:20: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:28:20: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:28:20: #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 13:28:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:28:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:28:24: 19000000 INFO @ Tue, 02 Aug 2022 13:28:31: 17000000 INFO @ Tue, 02 Aug 2022 13:28:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:28:35: 20000000 INFO @ Tue, 02 Aug 2022 13:28:42: 18000000 INFO @ Tue, 02 Aug 2022 13:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.05_summits.bed INFO @ Tue, 02 Aug 2022 13:28:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9882 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:28:46: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:28:46: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:28:46: #1 total tags in treatment: 7577217 INFO @ Tue, 02 Aug 2022 13:28:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:28:46: #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 13:28:46: #1 tags after filtering in treatment: 5529108 INFO @ Tue, 02 Aug 2022 13:28:46: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 13:28:46: #1 finished! INFO @ Tue, 02 Aug 2022 13:28:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:28:47: #2 number of paired peaks: 5871 INFO @ Tue, 02 Aug 2022 13:28:47: start model_add_line... INFO @ Tue, 02 Aug 2022 13:28:47: start X-correlation... INFO @ Tue, 02 Aug 2022 13:28:47: end of X-cor INFO @ Tue, 02 Aug 2022 13:28:47: #2 finished! INFO @ Tue, 02 Aug 2022 13:28:47: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:28:47: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.10_model.r WARNING @ Tue, 02 Aug 2022 13:28:47: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:28:47: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:28:47: #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 13:28:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:28:53: 19000000 INFO @ Tue, 02 Aug 2022 13:29:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:29:04: 20000000 INFO @ Tue, 02 Aug 2022 13:29:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:29:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:29:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.10_summits.bed INFO @ Tue, 02 Aug 2022 13:29:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7084 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:29:14: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:29:14: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:29:14: #1 total tags in treatment: 7577217 INFO @ Tue, 02 Aug 2022 13:29:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:29:14: #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 13:29:14: #1 tags after filtering in treatment: 5529108 INFO @ Tue, 02 Aug 2022 13:29:14: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 13:29:14: #1 finished! INFO @ Tue, 02 Aug 2022 13:29:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:29:15: #2 number of paired peaks: 5871 INFO @ Tue, 02 Aug 2022 13:29:15: start model_add_line... INFO @ Tue, 02 Aug 2022 13:29:15: start X-correlation... INFO @ Tue, 02 Aug 2022 13:29:15: end of X-cor INFO @ Tue, 02 Aug 2022 13:29:15: #2 finished! INFO @ Tue, 02 Aug 2022 13:29:15: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:29:15: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.20_model.r WARNING @ Tue, 02 Aug 2022 13:29:16: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:29:16: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:29:16: #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 13:29:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:29:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:29:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:29:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440708/SRX12440708.20_summits.bed INFO @ Tue, 02 Aug 2022 13:29:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3954 records, 4 fields): 161 millis CompletedMACS2peakCalling