Job ID = 16439877 SRX = SRX12175822 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32359640 spots for SRR15884961/SRR15884961.sra Written 32359640 spots for SRR15884961/SRR15884961.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440860 ("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: 01:24:46 32359640 reads; of these: 32359640 (100.00%) were paired; of these: 18398517 (56.86%) aligned concordantly 0 times 12260450 (37.89%) aligned concordantly exactly 1 time 1700673 (5.26%) aligned concordantly >1 times ---- 18398517 pairs aligned concordantly 0 times; of these: 3298346 (17.93%) aligned discordantly 1 time ---- 15100171 pairs aligned 0 times concordantly or discordantly; of these: 30200342 mates make up the pairs; of these: 28424924 (94.12%) aligned 0 times 869458 (2.88%) aligned exactly 1 time 905960 (3.00%) aligned >1 times 56.08% overall alignment rate Time searching: 01:24:47 Overall time: 01:24:47 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 28 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] 3307038 / 17179731 = 0.1925 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 18:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.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 18:19:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:19:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:19:15: 1000000 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 18:19:28: 2000000 INFO @ Tue, 02 Aug 2022 18:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.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 18:19:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:19:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:19:42: 3000000 INFO @ Tue, 02 Aug 2022 18:19:50: 1000000 INFO @ Tue, 02 Aug 2022 18:19:57: 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 18:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.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 18:20:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:20:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:20:09: 2000000 INFO @ Tue, 02 Aug 2022 18:20:12: 5000000 INFO @ Tue, 02 Aug 2022 18:20:17: 1000000 INFO @ Tue, 02 Aug 2022 18:20:28: 6000000 INFO @ Tue, 02 Aug 2022 18:20:28: 3000000 INFO @ Tue, 02 Aug 2022 18:20:33: 2000000 INFO @ Tue, 02 Aug 2022 18:20:44: 7000000 INFO @ Tue, 02 Aug 2022 18:20:47: 4000000 INFO @ Tue, 02 Aug 2022 18:20:49: 3000000 INFO @ Tue, 02 Aug 2022 18:21:00: 8000000 INFO @ Tue, 02 Aug 2022 18:21:04: 4000000 INFO @ Tue, 02 Aug 2022 18:21:07: 5000000 INFO @ Tue, 02 Aug 2022 18:21:16: 9000000 INFO @ Tue, 02 Aug 2022 18:21:20: 5000000 INFO @ Tue, 02 Aug 2022 18:21:29: 6000000 INFO @ Tue, 02 Aug 2022 18:21:32: 10000000 INFO @ Tue, 02 Aug 2022 18:21:35: 6000000 INFO @ Tue, 02 Aug 2022 18:21:49: 7000000 INFO @ Tue, 02 Aug 2022 18:21:52: 7000000 INFO @ Tue, 02 Aug 2022 18:21:53: 11000000 INFO @ Tue, 02 Aug 2022 18:22:08: 8000000 INFO @ Tue, 02 Aug 2022 18:22:08: 8000000 INFO @ Tue, 02 Aug 2022 18:22:11: 12000000 INFO @ Tue, 02 Aug 2022 18:22:25: 9000000 INFO @ Tue, 02 Aug 2022 18:22:26: 13000000 INFO @ Tue, 02 Aug 2022 18:22:27: 9000000 INFO @ Tue, 02 Aug 2022 18:22:41: 10000000 INFO @ Tue, 02 Aug 2022 18:22:42: 14000000 INFO @ Tue, 02 Aug 2022 18:22:47: 10000000 INFO @ Tue, 02 Aug 2022 18:22:56: 11000000 INFO @ Tue, 02 Aug 2022 18:22:58: 15000000 INFO @ Tue, 02 Aug 2022 18:23:06: 11000000 INFO @ Tue, 02 Aug 2022 18:23:12: 12000000 INFO @ Tue, 02 Aug 2022 18:23:15: 16000000 INFO @ Tue, 02 Aug 2022 18:23:26: 12000000 INFO @ Tue, 02 Aug 2022 18:23:28: 13000000 INFO @ Tue, 02 Aug 2022 18:23:31: 17000000 INFO @ Tue, 02 Aug 2022 18:23:44: 14000000 INFO @ Tue, 02 Aug 2022 18:23:45: 13000000 INFO @ Tue, 02 Aug 2022 18:23:54: 18000000 INFO @ Tue, 02 Aug 2022 18:24:00: 15000000 INFO @ Tue, 02 Aug 2022 18:24:04: 14000000 INFO @ Tue, 02 Aug 2022 18:24:16: 16000000 INFO @ Tue, 02 Aug 2022 18:24:17: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:24:22: 15000000 INFO @ Tue, 02 Aug 2022 18:24:33: 17000000 INFO @ Tue, 02 Aug 2022 18:24:34: 20000000 INFO @ Tue, 02 Aug 2022 18:24:40: 16000000 INFO @ Tue, 02 Aug 2022 18:24:49: 18000000 INFO @ Tue, 02 Aug 2022 18:24:50: 21000000 INFO @ Tue, 02 Aug 2022 18:24:58: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:25:06: 19000000 INFO @ Tue, 02 Aug 2022 18:25:06: 22000000 INFO @ Tue, 02 Aug 2022 18:25:16: 18000000 INFO @ Tue, 02 Aug 2022 18:25:22: 20000000 INFO @ Tue, 02 Aug 2022 18:25:22: 23000000 INFO @ Tue, 02 Aug 2022 18:25:36: 19000000 INFO @ Tue, 02 Aug 2022 18:25:37: 21000000 INFO @ Tue, 02 Aug 2022 18:25:37: 24000000 INFO @ Tue, 02 Aug 2022 18:25:52: 22000000 INFO @ Tue, 02 Aug 2022 18:25:53: 25000000 INFO @ Tue, 02 Aug 2022 18:25:56: 20000000 INFO @ Tue, 02 Aug 2022 18:26:08: 23000000 INFO @ Tue, 02 Aug 2022 18:26:09: 26000000 INFO @ Tue, 02 Aug 2022 18:26:15: 21000000 INFO @ Tue, 02 Aug 2022 18:26:24: 24000000 INFO @ Tue, 02 Aug 2022 18:26:25: 27000000 INFO @ Tue, 02 Aug 2022 18:26:33: 22000000 INFO @ Tue, 02 Aug 2022 18:26:41: 25000000 INFO @ Tue, 02 Aug 2022 18:26:41: 28000000 INFO @ Tue, 02 Aug 2022 18:26:52: 23000000 INFO @ Tue, 02 Aug 2022 18:26:57: 26000000 INFO @ Tue, 02 Aug 2022 18:26:57: 29000000 INFO @ Tue, 02 Aug 2022 18:27:08: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:27:08: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:27:08: #1 total tags in treatment: 11183961 INFO @ Tue, 02 Aug 2022 18:27:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:27:08: #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 18:27:09: #1 tags after filtering in treatment: 7165184 INFO @ Tue, 02 Aug 2022 18:27:09: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 18:27:09: #1 finished! INFO @ Tue, 02 Aug 2022 18:27:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:27:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:27:09: #2 number of paired peaks: 4747 INFO @ Tue, 02 Aug 2022 18:27:09: start model_add_line... INFO @ Tue, 02 Aug 2022 18:27:09: start X-correlation... INFO @ Tue, 02 Aug 2022 18:27:10: end of X-cor INFO @ Tue, 02 Aug 2022 18:27:10: #2 finished! INFO @ Tue, 02 Aug 2022 18:27:10: #2 predicted fragment length is 240 bps INFO @ Tue, 02 Aug 2022 18:27:10: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 02 Aug 2022 18:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.05_model.r WARNING @ Tue, 02 Aug 2022 18:27:10: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:27:10: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 02 Aug 2022 18:27:10: #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 18:27:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:27:11: 24000000 INFO @ Tue, 02 Aug 2022 18:27:13: 27000000 INFO @ Tue, 02 Aug 2022 18:27:29: 28000000 INFO @ Tue, 02 Aug 2022 18:27:30: 25000000 INFO @ Tue, 02 Aug 2022 18:27:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.05_summits.bed INFO @ Tue, 02 Aug 2022 18:27:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9612 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:27:44: 29000000 INFO @ Tue, 02 Aug 2022 18:27:49: 26000000 INFO @ Tue, 02 Aug 2022 18:27:54: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:27:54: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:27:54: #1 total tags in treatment: 11183961 INFO @ Tue, 02 Aug 2022 18:27:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:27:54: #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 18:27:55: #1 tags after filtering in treatment: 7165184 INFO @ Tue, 02 Aug 2022 18:27:55: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 18:27:55: #1 finished! INFO @ Tue, 02 Aug 2022 18:27:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:27:55: #2 number of paired peaks: 4747 INFO @ Tue, 02 Aug 2022 18:27:55: start model_add_line... INFO @ Tue, 02 Aug 2022 18:27:56: start X-correlation... INFO @ Tue, 02 Aug 2022 18:27:56: end of X-cor INFO @ Tue, 02 Aug 2022 18:27:56: #2 finished! INFO @ Tue, 02 Aug 2022 18:27:56: #2 predicted fragment length is 240 bps INFO @ Tue, 02 Aug 2022 18:27:56: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 02 Aug 2022 18:27:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.20_model.r WARNING @ Tue, 02 Aug 2022 18:27:56: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:27:56: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 02 Aug 2022 18:27:56: #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 18:27:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:27:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:28:07: 27000000 INFO @ Tue, 02 Aug 2022 18:28:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.20_summits.bed INFO @ Tue, 02 Aug 2022 18:28:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3951 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:28:27: 28000000 INFO @ Tue, 02 Aug 2022 18:28:45: 29000000 INFO @ Tue, 02 Aug 2022 18:28:57: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:28:57: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:28:57: #1 total tags in treatment: 11183961 INFO @ Tue, 02 Aug 2022 18:28:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:28:57: #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 18:28:58: #1 tags after filtering in treatment: 7165184 INFO @ Tue, 02 Aug 2022 18:28:58: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 18:28:58: #1 finished! INFO @ Tue, 02 Aug 2022 18:28:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:28:59: #2 number of paired peaks: 4747 INFO @ Tue, 02 Aug 2022 18:28:59: start model_add_line... INFO @ Tue, 02 Aug 2022 18:28:59: start X-correlation... INFO @ Tue, 02 Aug 2022 18:28:59: end of X-cor INFO @ Tue, 02 Aug 2022 18:28:59: #2 finished! INFO @ Tue, 02 Aug 2022 18:28:59: #2 predicted fragment length is 240 bps INFO @ Tue, 02 Aug 2022 18:28:59: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 02 Aug 2022 18:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.10_model.r WARNING @ Tue, 02 Aug 2022 18:28:59: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:28:59: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 02 Aug 2022 18:28:59: #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 18:28:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:29:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175822/SRX12175822.10_summits.bed INFO @ Tue, 02 Aug 2022 18:29:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6946 records, 4 fields): 34 millis CompletedMACS2peakCalling