Job ID = 16436396 SRX = SRX12440707 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:32:21 prefetch.2.10.7: 1) Downloading 'SRR16155888'... 2022-08-02T02:32:21 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:40:03 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:40:03 prefetch.2.10.7: 1) 'SRR16155888' was downloaded successfully 2022-08-02T02:40:03 prefetch.2.10.7: 'SRR16155888' has 0 unresolved dependencies Read 40233305 spots for SRR16155888/SRR16155888.sra Written 40233305 spots for SRR16155888/SRR16155888.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437629 ("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: 01:10:49 40233305 reads; of these: 40233305 (100.00%) were paired; of these: 30197855 (75.06%) aligned concordantly 0 times 8976823 (22.31%) aligned concordantly exactly 1 time 1058627 (2.63%) aligned concordantly >1 times ---- 30197855 pairs aligned concordantly 0 times; of these: 3380384 (11.19%) aligned discordantly 1 time ---- 26817471 pairs aligned 0 times concordantly or discordantly; of these: 53634942 mates make up the pairs; of these: 52111477 (97.16%) aligned 0 times 716714 (1.34%) aligned exactly 1 time 806751 (1.50%) aligned >1 times 35.24% overall alignment rate Time searching: 01:10:49 Overall time: 01:10:49 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] 2716506 / 13347090 = 0.2035 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 13:08:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.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 13:08:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:08:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:08:26: 1000000 INFO @ Tue, 02 Aug 2022 13:08:33: 2000000 INFO @ Tue, 02 Aug 2022 13:08:41: 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 13:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.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 13:08:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:08:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:08:49: 4000000 INFO @ Tue, 02 Aug 2022 13:08:58: 5000000 INFO @ Tue, 02 Aug 2022 13:08:58: 1000000 INFO @ Tue, 02 Aug 2022 13:09:06: 6000000 INFO @ Tue, 02 Aug 2022 13:09:07: 2000000 INFO @ Tue, 02 Aug 2022 13:09:14: 7000000 INFO @ Tue, 02 Aug 2022 13:09:15: 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 13:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.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 13:09:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:09:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:09:23: 8000000 INFO @ Tue, 02 Aug 2022 13:09:23: 4000000 INFO @ Tue, 02 Aug 2022 13:09:27: 1000000 INFO @ Tue, 02 Aug 2022 13:09:31: 9000000 INFO @ Tue, 02 Aug 2022 13:09:32: 5000000 INFO @ Tue, 02 Aug 2022 13:09:35: 2000000 INFO @ Tue, 02 Aug 2022 13:09:40: 10000000 INFO @ Tue, 02 Aug 2022 13:09:40: 6000000 INFO @ Tue, 02 Aug 2022 13:09:44: 3000000 INFO @ Tue, 02 Aug 2022 13:09:49: 7000000 INFO @ Tue, 02 Aug 2022 13:09:49: 11000000 INFO @ Tue, 02 Aug 2022 13:09:53: 4000000 INFO @ Tue, 02 Aug 2022 13:09:58: 8000000 INFO @ Tue, 02 Aug 2022 13:09:58: 12000000 INFO @ Tue, 02 Aug 2022 13:10:03: 5000000 INFO @ Tue, 02 Aug 2022 13:10:06: 9000000 INFO @ Tue, 02 Aug 2022 13:10:07: 13000000 INFO @ Tue, 02 Aug 2022 13:10:12: 6000000 INFO @ Tue, 02 Aug 2022 13:10:15: 10000000 INFO @ Tue, 02 Aug 2022 13:10:16: 14000000 INFO @ Tue, 02 Aug 2022 13:10:21: 7000000 INFO @ Tue, 02 Aug 2022 13:10:23: 11000000 INFO @ Tue, 02 Aug 2022 13:10:25: 15000000 INFO @ Tue, 02 Aug 2022 13:10:29: 8000000 INFO @ Tue, 02 Aug 2022 13:10:31: 12000000 INFO @ Tue, 02 Aug 2022 13:10:34: 16000000 INFO @ Tue, 02 Aug 2022 13:10:38: 9000000 INFO @ Tue, 02 Aug 2022 13:10:40: 13000000 INFO @ Tue, 02 Aug 2022 13:10:43: 17000000 INFO @ Tue, 02 Aug 2022 13:10:47: 10000000 INFO @ Tue, 02 Aug 2022 13:10:48: 14000000 INFO @ Tue, 02 Aug 2022 13:10:51: 18000000 INFO @ Tue, 02 Aug 2022 13:10:55: 11000000 INFO @ Tue, 02 Aug 2022 13:10:56: 15000000 INFO @ Tue, 02 Aug 2022 13:11:00: 19000000 INFO @ Tue, 02 Aug 2022 13:11:04: 12000000 INFO @ Tue, 02 Aug 2022 13:11:04: 16000000 INFO @ Tue, 02 Aug 2022 13:11:09: 20000000 INFO @ Tue, 02 Aug 2022 13:11:12: 13000000 INFO @ Tue, 02 Aug 2022 13:11:12: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:11:18: 21000000 INFO @ Tue, 02 Aug 2022 13:11:21: 14000000 INFO @ Tue, 02 Aug 2022 13:11:21: 18000000 INFO @ Tue, 02 Aug 2022 13:11:27: 22000000 INFO @ Tue, 02 Aug 2022 13:11:29: 15000000 INFO @ Tue, 02 Aug 2022 13:11:30: 19000000 INFO @ Tue, 02 Aug 2022 13:11:35: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:11:35: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:11:35: #1 total tags in treatment: 8005557 INFO @ Tue, 02 Aug 2022 13:11:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:11:35: #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 13:11:35: #1 tags after filtering in treatment: 5663459 INFO @ Tue, 02 Aug 2022 13:11:35: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 13:11:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:11:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:11:35: #2 number of paired peaks: 5840 INFO @ Tue, 02 Aug 2022 13:11:35: start model_add_line... INFO @ Tue, 02 Aug 2022 13:11:36: start X-correlation... INFO @ Tue, 02 Aug 2022 13:11:36: end of X-cor INFO @ Tue, 02 Aug 2022 13:11:36: #2 finished! INFO @ Tue, 02 Aug 2022 13:11:36: #2 predicted fragment length is 217 bps INFO @ Tue, 02 Aug 2022 13:11:36: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 02 Aug 2022 13:11:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.05_model.r WARNING @ Tue, 02 Aug 2022 13:11:36: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:11:36: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 02 Aug 2022 13:11:36: #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 13:11:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:11:38: 16000000 INFO @ Tue, 02 Aug 2022 13:11:38: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:11:47: 21000000 INFO @ Tue, 02 Aug 2022 13:11:47: 17000000 INFO @ Tue, 02 Aug 2022 13:11:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:11:55: 22000000 INFO @ Tue, 02 Aug 2022 13:11:55: 18000000 INFO @ Tue, 02 Aug 2022 13:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.05_summits.bed INFO @ Tue, 02 Aug 2022 13:11:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10319 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:12:03: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:12:03: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:12:03: #1 total tags in treatment: 8005557 INFO @ Tue, 02 Aug 2022 13:12:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:12:03: #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 13:12:03: #1 tags after filtering in treatment: 5663459 INFO @ Tue, 02 Aug 2022 13:12:03: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 13:12:03: #1 finished! INFO @ Tue, 02 Aug 2022 13:12:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:12:03: #2 number of paired peaks: 5840 INFO @ Tue, 02 Aug 2022 13:12:03: start model_add_line... INFO @ Tue, 02 Aug 2022 13:12:03: start X-correlation... INFO @ Tue, 02 Aug 2022 13:12:03: end of X-cor INFO @ Tue, 02 Aug 2022 13:12:03: #2 finished! INFO @ Tue, 02 Aug 2022 13:12:03: #2 predicted fragment length is 217 bps INFO @ Tue, 02 Aug 2022 13:12:03: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 02 Aug 2022 13:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.10_model.r WARNING @ Tue, 02 Aug 2022 13:12:04: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:12:04: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 02 Aug 2022 13:12:04: #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 13:12:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:12:04: 19000000 INFO @ Tue, 02 Aug 2022 13:12:11: 20000000 INFO @ Tue, 02 Aug 2022 13:12:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:12:18: 21000000 INFO @ Tue, 02 Aug 2022 13:12:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:12:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:12:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.10_summits.bed INFO @ Tue, 02 Aug 2022 13:12:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7290 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:12:26: 22000000 INFO @ Tue, 02 Aug 2022 13:12:32: #1 tag size is determined as 151 bps INFO @ Tue, 02 Aug 2022 13:12:32: #1 tag size = 151 INFO @ Tue, 02 Aug 2022 13:12:32: #1 total tags in treatment: 8005557 INFO @ Tue, 02 Aug 2022 13:12:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:12:32: #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 13:12:32: #1 tags after filtering in treatment: 5663459 INFO @ Tue, 02 Aug 2022 13:12:32: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 13:12:32: #1 finished! INFO @ Tue, 02 Aug 2022 13:12:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:12:33: #2 number of paired peaks: 5840 INFO @ Tue, 02 Aug 2022 13:12:33: start model_add_line... INFO @ Tue, 02 Aug 2022 13:12:33: start X-correlation... INFO @ Tue, 02 Aug 2022 13:12:33: end of X-cor INFO @ Tue, 02 Aug 2022 13:12:33: #2 finished! INFO @ Tue, 02 Aug 2022 13:12:33: #2 predicted fragment length is 217 bps INFO @ Tue, 02 Aug 2022 13:12:33: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 02 Aug 2022 13:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.20_model.r WARNING @ Tue, 02 Aug 2022 13:12:33: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:12:33: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 02 Aug 2022 13:12:33: #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 13:12:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:12:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:12:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12440707/SRX12440707.20_summits.bed INFO @ Tue, 02 Aug 2022 13:12:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3946 records, 4 fields): 48 millis CompletedMACS2peakCalling