Job ID = 16436392 SRX = SRX12440706 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:31:51 prefetch.2.10.7: 1) Downloading 'SRR16155887'... 2022-08-02T02:31:51 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:35:59 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:35:59 prefetch.2.10.7: 1) 'SRR16155887' was downloaded successfully 2022-08-02T02:35:59 prefetch.2.10.7: 'SRR16155887' has 0 unresolved dependencies Read 34290369 spots for SRR16155887/SRR16155887.sra Written 34290369 spots for SRR16155887/SRR16155887.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437578 ("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: 01:01:20 34290369 reads; of these: 34290369 (100.00%) were paired; of these: 25814627 (75.28%) aligned concordantly 0 times 7588390 (22.13%) aligned concordantly exactly 1 time 887352 (2.59%) aligned concordantly >1 times ---- 25814627 pairs aligned concordantly 0 times; of these: 2669429 (10.34%) aligned discordantly 1 time ---- 23145198 pairs aligned 0 times concordantly or discordantly; of these: 46290396 mates make up the pairs; of these: 45014095 (97.24%) aligned 0 times 651600 (1.41%) aligned exactly 1 time 624701 (1.35%) aligned >1 times 34.36% overall alignment rate Time searching: 01:01:20 Overall time: 01:01:20 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] 2020143 / 11092984 = 0.1821 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 12:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.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 12:51:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:51:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:51:55: 1000000 INFO @ Tue, 02 Aug 2022 12:52:02: 2000000 INFO @ Tue, 02 Aug 2022 12:52:09: 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 12:52:16: 4000000 INFO @ Tue, 02 Aug 2022 12:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.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 12:52:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:52:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:52:24: 5000000 INFO @ Tue, 02 Aug 2022 12:52:26: 1000000 INFO @ Tue, 02 Aug 2022 12:52:32: 6000000 INFO @ Tue, 02 Aug 2022 12:52:34: 2000000 INFO @ Tue, 02 Aug 2022 12:52:40: 7000000 INFO @ Tue, 02 Aug 2022 12:52:42: 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 12:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.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 12:52:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:52:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:52:48: 8000000 INFO @ Tue, 02 Aug 2022 12:52:50: 4000000 INFO @ Tue, 02 Aug 2022 12:52:56: 1000000 INFO @ Tue, 02 Aug 2022 12:52:57: 9000000 INFO @ Tue, 02 Aug 2022 12:52:58: 5000000 INFO @ Tue, 02 Aug 2022 12:53:04: 2000000 INFO @ Tue, 02 Aug 2022 12:53:05: 10000000 INFO @ Tue, 02 Aug 2022 12:53:06: 6000000 INFO @ Tue, 02 Aug 2022 12:53:12: 3000000 INFO @ Tue, 02 Aug 2022 12:53:13: 11000000 INFO @ Tue, 02 Aug 2022 12:53:15: 7000000 INFO @ Tue, 02 Aug 2022 12:53:20: 4000000 INFO @ Tue, 02 Aug 2022 12:53:21: 12000000 INFO @ Tue, 02 Aug 2022 12:53:23: 8000000 INFO @ Tue, 02 Aug 2022 12:53:28: 5000000 INFO @ Tue, 02 Aug 2022 12:53:29: 13000000 INFO @ Tue, 02 Aug 2022 12:53:31: 9000000 INFO @ Tue, 02 Aug 2022 12:53:36: 6000000 INFO @ Tue, 02 Aug 2022 12:53:37: 14000000 INFO @ Tue, 02 Aug 2022 12:53:39: 10000000 INFO @ Tue, 02 Aug 2022 12:53:44: 7000000 INFO @ Tue, 02 Aug 2022 12:53:45: 15000000 INFO @ Tue, 02 Aug 2022 12:53:47: 11000000 INFO @ Tue, 02 Aug 2022 12:53:52: 8000000 INFO @ Tue, 02 Aug 2022 12:53:53: 16000000 INFO @ Tue, 02 Aug 2022 12:53:55: 12000000 INFO @ Tue, 02 Aug 2022 12:54:00: 9000000 INFO @ Tue, 02 Aug 2022 12:54:01: 17000000 INFO @ Tue, 02 Aug 2022 12:54:03: 13000000 INFO @ Tue, 02 Aug 2022 12:54:08: 10000000 INFO @ Tue, 02 Aug 2022 12:54:09: 18000000 INFO @ Tue, 02 Aug 2022 12:54:10: 14000000 INFO @ Tue, 02 Aug 2022 12:54:16: 11000000 INFO @ Tue, 02 Aug 2022 12:54:17: 19000000 INFO @ Tue, 02 Aug 2022 12:54:18: 15000000 INFO @ Tue, 02 Aug 2022 12:54:21: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 12:54:21: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 12:54:21: #1 total tags in treatment: 6934120 INFO @ Tue, 02 Aug 2022 12:54:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:54:21: #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 12:54:21: #1 tags after filtering in treatment: 5297312 INFO @ Tue, 02 Aug 2022 12:54:21: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 12:54:21: #1 finished! INFO @ Tue, 02 Aug 2022 12:54:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:54:22: #2 number of paired peaks: 5376 INFO @ Tue, 02 Aug 2022 12:54:22: start model_add_line... INFO @ Tue, 02 Aug 2022 12:54:22: start X-correlation... INFO @ Tue, 02 Aug 2022 12:54:22: end of X-cor INFO @ Tue, 02 Aug 2022 12:54:22: #2 finished! INFO @ Tue, 02 Aug 2022 12:54:22: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 12:54:22: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 12:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.05_model.r WARNING @ Tue, 02 Aug 2022 12:54:22: #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 12:54:22: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 12:54:22: #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 12:54:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:54:24: 12000000 INFO @ Tue, 02 Aug 2022 12:54:27: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:54:32: 13000000 INFO @ Tue, 02 Aug 2022 12:54:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:54:34: 17000000 INFO @ Tue, 02 Aug 2022 12:54:40: 14000000 INFO @ Tue, 02 Aug 2022 12:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.05_summits.bed INFO @ Tue, 02 Aug 2022 12:54:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9410 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:54:42: 18000000 INFO @ Tue, 02 Aug 2022 12:54:48: 15000000 INFO @ Tue, 02 Aug 2022 12:54:50: 19000000 INFO @ Tue, 02 Aug 2022 12:54:54: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 12:54:54: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 12:54:54: #1 total tags in treatment: 6934120 INFO @ Tue, 02 Aug 2022 12:54:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:54:54: #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 12:54:54: #1 tags after filtering in treatment: 5297312 INFO @ Tue, 02 Aug 2022 12:54:54: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 12:54:54: #1 finished! INFO @ Tue, 02 Aug 2022 12:54:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:54:55: #2 number of paired peaks: 5376 INFO @ Tue, 02 Aug 2022 12:54:55: start model_add_line... INFO @ Tue, 02 Aug 2022 12:54:55: start X-correlation... INFO @ Tue, 02 Aug 2022 12:54:55: end of X-cor INFO @ Tue, 02 Aug 2022 12:54:55: #2 finished! INFO @ Tue, 02 Aug 2022 12:54:55: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 12:54:55: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 12:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.10_model.r WARNING @ Tue, 02 Aug 2022 12:54:55: #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 12:54:55: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 12:54:55: #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 12:54:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:54:56: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:55:03: 17000000 INFO @ Tue, 02 Aug 2022 12:55:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:55:10: 18000000 INFO @ Tue, 02 Aug 2022 12:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.10_summits.bed INFO @ Tue, 02 Aug 2022 12:55:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6408 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:55:17: 19000000 INFO @ Tue, 02 Aug 2022 12:55:21: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 12:55:21: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 12:55:21: #1 total tags in treatment: 6934120 INFO @ Tue, 02 Aug 2022 12:55:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:55:21: #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 12:55:21: #1 tags after filtering in treatment: 5297312 INFO @ Tue, 02 Aug 2022 12:55:21: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 12:55:21: #1 finished! INFO @ Tue, 02 Aug 2022 12:55:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:55:22: #2 number of paired peaks: 5376 INFO @ Tue, 02 Aug 2022 12:55:22: start model_add_line... INFO @ Tue, 02 Aug 2022 12:55:22: start X-correlation... INFO @ Tue, 02 Aug 2022 12:55:22: end of X-cor INFO @ Tue, 02 Aug 2022 12:55:22: #2 finished! INFO @ Tue, 02 Aug 2022 12:55:22: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 12:55:22: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 12:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.20_model.r WARNING @ Tue, 02 Aug 2022 12:55:22: #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 12:55:22: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 12:55:22: #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 12:55:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:55:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:55:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440706/SRX12440706.20_summits.bed INFO @ Tue, 02 Aug 2022 12:55:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3363 records, 4 fields): 59 millis CompletedMACS2peakCalling