Job ID = 16436382 SRX = SRX12440704 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:29:15 prefetch.2.10.7: 1) Downloading 'SRR16155885'... 2022-08-02T02:29:15 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:32:56 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:32:56 prefetch.2.10.7: 1) 'SRR16155885' was downloaded successfully 2022-08-02T02:32:56 prefetch.2.10.7: 'SRR16155885' has 0 unresolved dependencies Read 32539714 spots for SRR16155885/SRR16155885.sra Written 32539714 spots for SRR16155885/SRR16155885.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437939 ("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: 01:29:30 32539714 reads; of these: 32539714 (100.00%) were paired; of these: 24074227 (73.98%) aligned concordantly 0 times 7511707 (23.08%) aligned concordantly exactly 1 time 953780 (2.93%) aligned concordantly >1 times ---- 24074227 pairs aligned concordantly 0 times; of these: 2773562 (11.52%) aligned discordantly 1 time ---- 21300665 pairs aligned 0 times concordantly or discordantly; of these: 42601330 mates make up the pairs; of these: 41328992 (97.01%) aligned 0 times 572483 (1.34%) aligned exactly 1 time 699855 (1.64%) aligned >1 times 36.49% overall alignment rate Time searching: 01:29:31 Overall time: 01:29:31 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] 2113364 / 11183304 = 0.1890 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 13:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.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 13:22:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:22:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:22:23: 1000000 INFO @ Tue, 02 Aug 2022 13:22:31: 2000000 INFO @ Tue, 02 Aug 2022 13:22:39: 3000000 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 13:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.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 13:22:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:22:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:22:48: 4000000 INFO @ Tue, 02 Aug 2022 13:22:53: 1000000 INFO @ Tue, 02 Aug 2022 13:22:57: 5000000 INFO @ Tue, 02 Aug 2022 13:23:02: 2000000 INFO @ Tue, 02 Aug 2022 13:23:06: 6000000 INFO @ Tue, 02 Aug 2022 13:23:12: 3000000 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 13:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.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 13:23:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:23:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:23:15: 7000000 INFO @ Tue, 02 Aug 2022 13:23:21: 4000000 INFO @ Tue, 02 Aug 2022 13:23:24: 1000000 INFO @ Tue, 02 Aug 2022 13:23:26: 8000000 INFO @ Tue, 02 Aug 2022 13:23:30: 5000000 INFO @ Tue, 02 Aug 2022 13:23:32: 2000000 INFO @ Tue, 02 Aug 2022 13:23:36: 9000000 INFO @ Tue, 02 Aug 2022 13:23:40: 6000000 INFO @ Tue, 02 Aug 2022 13:23:41: 3000000 INFO @ Tue, 02 Aug 2022 13:23:45: 10000000 INFO @ Tue, 02 Aug 2022 13:23:50: 7000000 INFO @ Tue, 02 Aug 2022 13:23:50: 4000000 INFO @ Tue, 02 Aug 2022 13:23:55: 11000000 INFO @ Tue, 02 Aug 2022 13:23:58: 5000000 INFO @ Tue, 02 Aug 2022 13:23:59: 8000000 INFO @ Tue, 02 Aug 2022 13:24:05: 12000000 INFO @ Tue, 02 Aug 2022 13:24:07: 6000000 INFO @ Tue, 02 Aug 2022 13:24:09: 9000000 INFO @ Tue, 02 Aug 2022 13:24:15: 13000000 INFO @ Tue, 02 Aug 2022 13:24:16: 7000000 INFO @ Tue, 02 Aug 2022 13:24:19: 10000000 INFO @ Tue, 02 Aug 2022 13:24:25: 14000000 INFO @ Tue, 02 Aug 2022 13:24:27: 8000000 INFO @ Tue, 02 Aug 2022 13:24:29: 11000000 INFO @ Tue, 02 Aug 2022 13:24:34: 15000000 INFO @ Tue, 02 Aug 2022 13:24:39: 9000000 INFO @ Tue, 02 Aug 2022 13:24:40: 12000000 INFO @ Tue, 02 Aug 2022 13:24:44: 16000000 INFO @ Tue, 02 Aug 2022 13:24:50: 13000000 INFO @ Tue, 02 Aug 2022 13:24:51: 10000000 INFO @ Tue, 02 Aug 2022 13:24:54: 17000000 INFO @ Tue, 02 Aug 2022 13:25:01: 14000000 INFO @ Tue, 02 Aug 2022 13:25:02: 11000000 INFO @ Tue, 02 Aug 2022 13:25:04: 18000000 INFO @ Tue, 02 Aug 2022 13:25:11: 15000000 INFO @ Tue, 02 Aug 2022 13:25:13: 12000000 INFO @ Tue, 02 Aug 2022 13:25:18: 19000000 INFO @ Tue, 02 Aug 2022 13:25:22: 16000000 INFO @ Tue, 02 Aug 2022 13:25:23: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:25:23: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:25:23: #1 total tags in treatment: 6871491 INFO @ Tue, 02 Aug 2022 13:25:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:25:23: #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 13:25:23: #1 tags after filtering in treatment: 4857790 INFO @ Tue, 02 Aug 2022 13:25:23: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 13:25:23: #1 finished! INFO @ Tue, 02 Aug 2022 13:25:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:25:24: 13000000 INFO @ Tue, 02 Aug 2022 13:25:24: #2 number of paired peaks: 6808 INFO @ Tue, 02 Aug 2022 13:25:24: start model_add_line... INFO @ Tue, 02 Aug 2022 13:25:24: start X-correlation... INFO @ Tue, 02 Aug 2022 13:25:24: end of X-cor INFO @ Tue, 02 Aug 2022 13:25:24: #2 finished! INFO @ Tue, 02 Aug 2022 13:25:24: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:25:24: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.05_model.r WARNING @ Tue, 02 Aug 2022 13:25:24: #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 13:25:24: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:25:24: #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 13:25:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:25:32: 17000000 INFO @ Tue, 02 Aug 2022 13:25:35: 14000000 INFO @ Tue, 02 Aug 2022 13:25:37: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:25:43: 18000000 INFO @ Tue, 02 Aug 2022 13:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.05_summits.bed INFO @ Tue, 02 Aug 2022 13:25:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9770 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:25:46: 15000000 INFO @ Tue, 02 Aug 2022 13:25:53: 19000000 INFO @ Tue, 02 Aug 2022 13:25:57: 16000000 INFO @ Tue, 02 Aug 2022 13:25:58: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:25:58: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:25:58: #1 total tags in treatment: 6871491 INFO @ Tue, 02 Aug 2022 13:25:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:25:58: #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 13:25:58: #1 tags after filtering in treatment: 4857790 INFO @ Tue, 02 Aug 2022 13:25:58: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 13:25:58: #1 finished! INFO @ Tue, 02 Aug 2022 13:25:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:25:59: #2 number of paired peaks: 6808 INFO @ Tue, 02 Aug 2022 13:25:59: start model_add_line... INFO @ Tue, 02 Aug 2022 13:25:59: start X-correlation... INFO @ Tue, 02 Aug 2022 13:25:59: end of X-cor INFO @ Tue, 02 Aug 2022 13:25:59: #2 finished! INFO @ Tue, 02 Aug 2022 13:25:59: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:25:59: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.10_model.r WARNING @ Tue, 02 Aug 2022 13:25:59: #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 13:25:59: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:25:59: #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 13:25:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:26:07: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:26:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:26:17: 18000000 INFO @ Tue, 02 Aug 2022 13:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.10_summits.bed INFO @ Tue, 02 Aug 2022 13:26:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6923 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:26:28: 19000000 INFO @ Tue, 02 Aug 2022 13:26:33: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:26:33: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:26:33: #1 total tags in treatment: 6871491 INFO @ Tue, 02 Aug 2022 13:26:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:26:33: #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 13:26:33: #1 tags after filtering in treatment: 4857790 INFO @ Tue, 02 Aug 2022 13:26:33: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 13:26:33: #1 finished! INFO @ Tue, 02 Aug 2022 13:26:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:26:34: #2 number of paired peaks: 6808 INFO @ Tue, 02 Aug 2022 13:26:34: start model_add_line... INFO @ Tue, 02 Aug 2022 13:26:34: start X-correlation... INFO @ Tue, 02 Aug 2022 13:26:34: end of X-cor INFO @ Tue, 02 Aug 2022 13:26:34: #2 finished! INFO @ Tue, 02 Aug 2022 13:26:34: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 13:26:34: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 13:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.20_model.r WARNING @ Tue, 02 Aug 2022 13:26:34: #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 13:26:34: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 13:26:34: #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 13:26:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:26:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440704/SRX12440704.20_summits.bed INFO @ Tue, 02 Aug 2022 13:26:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3866 records, 4 fields): 23 millis CompletedMACS2peakCalling