Job ID = 16439645 SRX = SRX12375847 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36008438 spots for SRR16089462/SRR16089462.sra Written 36008438 spots for SRR16089462/SRR16089462.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440145 ("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: 01:27:17 36008438 reads; of these: 36008438 (100.00%) were paired; of these: 10412395 (28.92%) aligned concordantly 0 times 23747292 (65.95%) aligned concordantly exactly 1 time 1848751 (5.13%) aligned concordantly >1 times ---- 10412395 pairs aligned concordantly 0 times; of these: 5784945 (55.56%) aligned discordantly 1 time ---- 4627450 pairs aligned 0 times concordantly or discordantly; of these: 9254900 mates make up the pairs; of these: 6196576 (66.95%) aligned 0 times 1520620 (16.43%) aligned exactly 1 time 1537704 (16.62%) aligned >1 times 91.40% overall alignment rate Time searching: 01:27:17 Overall time: 01:27:17 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 48 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] 20832544 / 31267025 = 0.6663 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 17:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.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 17:36:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:36:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:36:42: 1000000 INFO @ Tue, 02 Aug 2022 17:36:49: 2000000 INFO @ Tue, 02 Aug 2022 17:36:57: 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 17:37:04: 4000000 INFO @ Tue, 02 Aug 2022 17:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.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 17:37:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:37:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:37:10: 1000000 INFO @ Tue, 02 Aug 2022 17:37:11: 5000000 INFO @ Tue, 02 Aug 2022 17:37:17: 2000000 INFO @ Tue, 02 Aug 2022 17:37:19: 6000000 INFO @ Tue, 02 Aug 2022 17:37:24: 3000000 INFO @ Tue, 02 Aug 2022 17:37:26: 7000000 INFO @ Tue, 02 Aug 2022 17:37:30: 4000000 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 17:37:33: 8000000 INFO @ Tue, 02 Aug 2022 17:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.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 17:37:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:37:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:37:37: 5000000 INFO @ Tue, 02 Aug 2022 17:37:40: 1000000 INFO @ Tue, 02 Aug 2022 17:37:41: 9000000 INFO @ Tue, 02 Aug 2022 17:37:43: 6000000 INFO @ Tue, 02 Aug 2022 17:37:47: 2000000 INFO @ Tue, 02 Aug 2022 17:37:49: 10000000 INFO @ Tue, 02 Aug 2022 17:37:50: 7000000 INFO @ Tue, 02 Aug 2022 17:37:54: 3000000 INFO @ Tue, 02 Aug 2022 17:37:57: 8000000 INFO @ Tue, 02 Aug 2022 17:37:57: 11000000 INFO @ Tue, 02 Aug 2022 17:38:01: 4000000 INFO @ Tue, 02 Aug 2022 17:38:03: 9000000 INFO @ Tue, 02 Aug 2022 17:38:04: 12000000 INFO @ Tue, 02 Aug 2022 17:38:07: 5000000 INFO @ Tue, 02 Aug 2022 17:38:10: 10000000 INFO @ Tue, 02 Aug 2022 17:38:13: 13000000 INFO @ Tue, 02 Aug 2022 17:38:15: 6000000 INFO @ Tue, 02 Aug 2022 17:38:17: 11000000 INFO @ Tue, 02 Aug 2022 17:38:21: 14000000 INFO @ Tue, 02 Aug 2022 17:38:22: 7000000 INFO @ Tue, 02 Aug 2022 17:38:24: 12000000 INFO @ Tue, 02 Aug 2022 17:38:28: 15000000 INFO @ Tue, 02 Aug 2022 17:38:29: 8000000 INFO @ Tue, 02 Aug 2022 17:38:31: 13000000 INFO @ Tue, 02 Aug 2022 17:38:36: 9000000 INFO @ Tue, 02 Aug 2022 17:38:36: 16000000 INFO @ Tue, 02 Aug 2022 17:38:38: 14000000 INFO @ Tue, 02 Aug 2022 17:38:43: 10000000 INFO @ Tue, 02 Aug 2022 17:38:44: 17000000 INFO @ Tue, 02 Aug 2022 17:38:45: 15000000 INFO @ Tue, 02 Aug 2022 17:38:50: 11000000 INFO @ Tue, 02 Aug 2022 17:38:52: 18000000 INFO @ Tue, 02 Aug 2022 17:38:52: 16000000 INFO @ Tue, 02 Aug 2022 17:38:57: 12000000 INFO @ Tue, 02 Aug 2022 17:38:59: 17000000 INFO @ Tue, 02 Aug 2022 17:39:00: 19000000 INFO @ Tue, 02 Aug 2022 17:39:04: 13000000 INFO @ Tue, 02 Aug 2022 17:39:07: 18000000 INFO @ Tue, 02 Aug 2022 17:39:08: 20000000 INFO @ Tue, 02 Aug 2022 17:39:11: 14000000 INFO @ Tue, 02 Aug 2022 17:39:14: 19000000 INFO @ Tue, 02 Aug 2022 17:39:15: 21000000 INFO @ Tue, 02 Aug 2022 17:39:18: 15000000 INFO @ Tue, 02 Aug 2022 17:39:21: 20000000 INFO @ Tue, 02 Aug 2022 17:39:23: 22000000 INFO @ Tue, 02 Aug 2022 17:39:25: 16000000 INFO @ Tue, 02 Aug 2022 17:39:28: 21000000 INFO @ Tue, 02 Aug 2022 17:39:31: 23000000 INFO @ Tue, 02 Aug 2022 17:39:32: 17000000 INFO @ Tue, 02 Aug 2022 17:39:35: 22000000 INFO @ Tue, 02 Aug 2022 17:39:39: 24000000 INFO @ Tue, 02 Aug 2022 17:39:39: 18000000 INFO @ Tue, 02 Aug 2022 17:39:40: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:39:40: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:39:40: #1 total tags in treatment: 7763704 INFO @ Tue, 02 Aug 2022 17:39:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:39:40: #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 17:39:40: #1 tags after filtering in treatment: 7462268 INFO @ Tue, 02 Aug 2022 17:39:40: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 17:39:40: #1 finished! INFO @ Tue, 02 Aug 2022 17:39:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:39:40: #2 number of paired peaks: 797 WARNING @ Tue, 02 Aug 2022 17:39:40: Fewer paired peaks (797) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 797 pairs to build model! INFO @ Tue, 02 Aug 2022 17:39:40: start model_add_line... INFO @ Tue, 02 Aug 2022 17:39:41: start X-correlation... INFO @ Tue, 02 Aug 2022 17:39:41: end of X-cor INFO @ Tue, 02 Aug 2022 17:39:41: #2 finished! INFO @ Tue, 02 Aug 2022 17:39:41: #2 predicted fragment length is 255 bps INFO @ Tue, 02 Aug 2022 17:39:41: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 02 Aug 2022 17:39:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.05_model.r WARNING @ Tue, 02 Aug 2022 17:39:41: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:39:41: #2 You may need to consider one of the other alternative d(s): 255 WARNING @ Tue, 02 Aug 2022 17:39:41: #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 17:39:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:39:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:39:42: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:39:46: 19000000 INFO @ Tue, 02 Aug 2022 17:39:49: 24000000 INFO @ Tue, 02 Aug 2022 17:39:50: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:39:50: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:39:50: #1 total tags in treatment: 7763704 INFO @ Tue, 02 Aug 2022 17:39:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:39:50: #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 17:39:50: #1 tags after filtering in treatment: 7462268 INFO @ Tue, 02 Aug 2022 17:39:50: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 17:39:50: #1 finished! INFO @ Tue, 02 Aug 2022 17:39:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:39:50: #2 number of paired peaks: 797 WARNING @ Tue, 02 Aug 2022 17:39:50: Fewer paired peaks (797) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 797 pairs to build model! INFO @ Tue, 02 Aug 2022 17:39:50: start model_add_line... INFO @ Tue, 02 Aug 2022 17:39:50: start X-correlation... INFO @ Tue, 02 Aug 2022 17:39:50: end of X-cor INFO @ Tue, 02 Aug 2022 17:39:50: #2 finished! INFO @ Tue, 02 Aug 2022 17:39:50: #2 predicted fragment length is 255 bps INFO @ Tue, 02 Aug 2022 17:39:50: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 02 Aug 2022 17:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.10_model.r WARNING @ Tue, 02 Aug 2022 17:39:51: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:39:51: #2 You may need to consider one of the other alternative d(s): 255 WARNING @ Tue, 02 Aug 2022 17:39:51: #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 17:39:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:39:53: 20000000 INFO @ Tue, 02 Aug 2022 17:39:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:39:59: 21000000 INFO @ Tue, 02 Aug 2022 17:40:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.05_summits.bed INFO @ Tue, 02 Aug 2022 17:40:06: Done! INFO @ Tue, 02 Aug 2022 17:40:06: 22000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3969 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:40:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:40:12: 23000000 INFO @ Tue, 02 Aug 2022 17:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.10_summits.bed INFO @ Tue, 02 Aug 2022 17:40:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1740 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:40:19: 24000000 INFO @ Tue, 02 Aug 2022 17:40:20: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:40:20: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:40:20: #1 total tags in treatment: 7763704 INFO @ Tue, 02 Aug 2022 17:40:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:40:20: #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 17:40:20: #1 tags after filtering in treatment: 7462268 INFO @ Tue, 02 Aug 2022 17:40:20: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 17:40:20: #1 finished! INFO @ Tue, 02 Aug 2022 17:40:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:40:20: #2 number of paired peaks: 797 WARNING @ Tue, 02 Aug 2022 17:40:20: Fewer paired peaks (797) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 797 pairs to build model! INFO @ Tue, 02 Aug 2022 17:40:20: start model_add_line... INFO @ Tue, 02 Aug 2022 17:40:21: start X-correlation... INFO @ Tue, 02 Aug 2022 17:40:21: end of X-cor INFO @ Tue, 02 Aug 2022 17:40:21: #2 finished! INFO @ Tue, 02 Aug 2022 17:40:21: #2 predicted fragment length is 255 bps INFO @ Tue, 02 Aug 2022 17:40:21: #2 alternative fragment length(s) may be 255 bps INFO @ Tue, 02 Aug 2022 17:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.20_model.r WARNING @ Tue, 02 Aug 2022 17:40:21: #2 Since the d (255) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:40:21: #2 You may need to consider one of the other alternative d(s): 255 WARNING @ Tue, 02 Aug 2022 17:40:21: #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 17:40:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:40:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:40:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12375847/SRX12375847.20_summits.bed INFO @ Tue, 02 Aug 2022 17:40:45: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (504 records, 4 fields): 31 millis CompletedMACS2peakCalling