Job ID = 16436374 SRX = SRX12440701 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:26:44 prefetch.2.10.7: 1) Downloading 'SRR16155882'... 2022-08-02T02:26:44 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:31:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:31:51 prefetch.2.10.7: 1) 'SRR16155882' was downloaded successfully 2022-08-02T02:31:51 prefetch.2.10.7: 'SRR16155882' has 0 unresolved dependencies Read 42686442 spots for SRR16155882/SRR16155882.sra Written 42686442 spots for SRR16155882/SRR16155882.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437616 ("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: 01:15:30 42686442 reads; of these: 42686442 (100.00%) were paired; of these: 32234587 (75.51%) aligned concordantly 0 times 9438185 (22.11%) aligned concordantly exactly 1 time 1013670 (2.37%) aligned concordantly >1 times ---- 32234587 pairs aligned concordantly 0 times; of these: 3307676 (10.26%) aligned discordantly 1 time ---- 28926911 pairs aligned 0 times concordantly or discordantly; of these: 57853822 mates make up the pairs; of these: 56360554 (97.42%) aligned 0 times 780173 (1.35%) aligned exactly 1 time 713095 (1.23%) aligned >1 times 33.98% overall alignment rate Time searching: 01:15:30 Overall time: 01:15:30 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] 2604416 / 13692464 = 0.1902 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 13:04:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.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 13:04:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:04:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:04:34: 1000000 INFO @ Tue, 02 Aug 2022 13:04:43: 2000000 INFO @ Tue, 02 Aug 2022 13:04:52: 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 13:04:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.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 13:04:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:04:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:05:01: 4000000 INFO @ Tue, 02 Aug 2022 13:05:03: 1000000 INFO @ Tue, 02 Aug 2022 13:05:11: 5000000 INFO @ Tue, 02 Aug 2022 13:05:12: 2000000 INFO @ Tue, 02 Aug 2022 13:05:20: 6000000 INFO @ Tue, 02 Aug 2022 13:05:21: 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 13:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.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 13:05:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:05:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:05:29: 7000000 INFO @ Tue, 02 Aug 2022 13:05:30: 4000000 INFO @ Tue, 02 Aug 2022 13:05:34: 1000000 INFO @ Tue, 02 Aug 2022 13:05:39: 8000000 INFO @ Tue, 02 Aug 2022 13:05:39: 5000000 INFO @ Tue, 02 Aug 2022 13:05:43: 2000000 INFO @ Tue, 02 Aug 2022 13:05:49: 6000000 INFO @ Tue, 02 Aug 2022 13:05:49: 9000000 INFO @ Tue, 02 Aug 2022 13:05:53: 3000000 INFO @ Tue, 02 Aug 2022 13:05:58: 7000000 INFO @ Tue, 02 Aug 2022 13:05:59: 10000000 INFO @ Tue, 02 Aug 2022 13:06:02: 4000000 INFO @ Tue, 02 Aug 2022 13:06:07: 8000000 INFO @ Tue, 02 Aug 2022 13:06:09: 11000000 INFO @ Tue, 02 Aug 2022 13:06:12: 5000000 INFO @ Tue, 02 Aug 2022 13:06:16: 9000000 INFO @ Tue, 02 Aug 2022 13:06:19: 12000000 INFO @ Tue, 02 Aug 2022 13:06:21: 6000000 INFO @ Tue, 02 Aug 2022 13:06:25: 10000000 INFO @ Tue, 02 Aug 2022 13:06:29: 13000000 INFO @ Tue, 02 Aug 2022 13:06:31: 7000000 INFO @ Tue, 02 Aug 2022 13:06:34: 11000000 INFO @ Tue, 02 Aug 2022 13:06:39: 14000000 INFO @ Tue, 02 Aug 2022 13:06:40: 8000000 INFO @ Tue, 02 Aug 2022 13:06:44: 12000000 INFO @ Tue, 02 Aug 2022 13:06:49: 15000000 INFO @ Tue, 02 Aug 2022 13:06:50: 9000000 INFO @ Tue, 02 Aug 2022 13:06:54: 13000000 INFO @ Tue, 02 Aug 2022 13:06:59: 16000000 INFO @ Tue, 02 Aug 2022 13:07:00: 10000000 INFO @ Tue, 02 Aug 2022 13:07:04: 14000000 INFO @ Tue, 02 Aug 2022 13:07:10: 11000000 INFO @ Tue, 02 Aug 2022 13:07:10: 17000000 INFO @ Tue, 02 Aug 2022 13:07:14: 15000000 INFO @ Tue, 02 Aug 2022 13:07:19: 12000000 INFO @ Tue, 02 Aug 2022 13:07:20: 18000000 INFO @ Tue, 02 Aug 2022 13:07:24: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:07:28: 13000000 INFO @ Tue, 02 Aug 2022 13:07:30: 19000000 INFO @ Tue, 02 Aug 2022 13:07:35: 17000000 INFO @ Tue, 02 Aug 2022 13:07:37: 14000000 INFO @ Tue, 02 Aug 2022 13:07:41: 20000000 INFO @ Tue, 02 Aug 2022 13:07:46: 18000000 INFO @ Tue, 02 Aug 2022 13:07:46: 15000000 INFO @ Tue, 02 Aug 2022 13:07:52: 21000000 INFO @ Tue, 02 Aug 2022 13:07:54: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:07:56: 19000000 INFO @ Tue, 02 Aug 2022 13:08:02: 22000000 INFO @ Tue, 02 Aug 2022 13:08:03: 17000000 INFO @ Tue, 02 Aug 2022 13:08:07: 20000000 INFO @ Tue, 02 Aug 2022 13:08:12: 18000000 INFO @ Tue, 02 Aug 2022 13:08:13: 23000000 INFO @ Tue, 02 Aug 2022 13:08:18: 21000000 INFO @ Tue, 02 Aug 2022 13:08:20: 19000000 INFO @ Tue, 02 Aug 2022 13:08:21: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:08:21: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:08:21: #1 total tags in treatment: 8494314 INFO @ Tue, 02 Aug 2022 13:08:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:08:21: #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 13:08:21: #1 tags after filtering in treatment: 6199668 INFO @ Tue, 02 Aug 2022 13:08:21: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 13:08:21: #1 finished! INFO @ Tue, 02 Aug 2022 13:08:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:08:21: #2 number of paired peaks: 5431 INFO @ Tue, 02 Aug 2022 13:08:21: start model_add_line... INFO @ Tue, 02 Aug 2022 13:08:21: start X-correlation... INFO @ Tue, 02 Aug 2022 13:08:22: end of X-cor INFO @ Tue, 02 Aug 2022 13:08:22: #2 finished! INFO @ Tue, 02 Aug 2022 13:08:22: #2 predicted fragment length is 214 bps INFO @ Tue, 02 Aug 2022 13:08:22: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 02 Aug 2022 13:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.05_model.r WARNING @ Tue, 02 Aug 2022 13:08:22: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:08:22: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 02 Aug 2022 13:08:22: #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 13:08:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:08:28: 22000000 INFO @ Tue, 02 Aug 2022 13:08:29: 20000000 INFO @ Tue, 02 Aug 2022 13:08:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:08:38: 21000000 INFO @ Tue, 02 Aug 2022 13:08:39: 23000000 INFO @ Tue, 02 Aug 2022 13:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.05_summits.bed INFO @ Tue, 02 Aug 2022 13:08:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10257 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:08:46: 22000000 INFO @ Tue, 02 Aug 2022 13:08:47: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:08:47: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:08:47: #1 total tags in treatment: 8494314 INFO @ Tue, 02 Aug 2022 13:08:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:08:47: #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 13:08:47: #1 tags after filtering in treatment: 6199668 INFO @ Tue, 02 Aug 2022 13:08:47: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 13:08:47: #1 finished! INFO @ Tue, 02 Aug 2022 13:08:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:08:48: #2 number of paired peaks: 5431 INFO @ Tue, 02 Aug 2022 13:08:48: start model_add_line... INFO @ Tue, 02 Aug 2022 13:08:48: start X-correlation... INFO @ Tue, 02 Aug 2022 13:08:48: end of X-cor INFO @ Tue, 02 Aug 2022 13:08:48: #2 finished! INFO @ Tue, 02 Aug 2022 13:08:48: #2 predicted fragment length is 214 bps INFO @ Tue, 02 Aug 2022 13:08:48: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 02 Aug 2022 13:08:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.10_model.r WARNING @ Tue, 02 Aug 2022 13:08:48: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:08:48: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 02 Aug 2022 13:08:48: #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 13:08:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:08:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:08:54: 23000000 INFO @ Tue, 02 Aug 2022 13:09:01: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:09:01: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:09:01: #1 total tags in treatment: 8494314 INFO @ Tue, 02 Aug 2022 13:09:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:09:01: #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 13:09:01: #1 tags after filtering in treatment: 6199668 INFO @ Tue, 02 Aug 2022 13:09:01: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 02 Aug 2022 13:09:01: #1 finished! INFO @ Tue, 02 Aug 2022 13:09:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:09:01: #2 number of paired peaks: 5431 INFO @ Tue, 02 Aug 2022 13:09:01: start model_add_line... INFO @ Tue, 02 Aug 2022 13:09:02: start X-correlation... INFO @ Tue, 02 Aug 2022 13:09:02: end of X-cor INFO @ Tue, 02 Aug 2022 13:09:02: #2 finished! INFO @ Tue, 02 Aug 2022 13:09:02: #2 predicted fragment length is 214 bps INFO @ Tue, 02 Aug 2022 13:09:02: #2 alternative fragment length(s) may be 214 bps INFO @ Tue, 02 Aug 2022 13:09:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.20_model.r WARNING @ Tue, 02 Aug 2022 13:09:02: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:09:02: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Tue, 02 Aug 2022 13:09:02: #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 13:09:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:09:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:09:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.10_summits.bed INFO @ Tue, 02 Aug 2022 13:09:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7242 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:09:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440701/SRX12440701.20_summits.bed INFO @ Tue, 02 Aug 2022 13:09:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3920 records, 4 fields): 41 millis CompletedMACS2peakCalling