Job ID = 16437218 SRX = SRX12119063 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35355212 spots for SRR15827101/SRR15827101.sra Written 35355212 spots for SRR15827101/SRR15827101.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438586 ("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: 01:29:00 35355212 reads; of these: 35355212 (100.00%) were paired; of these: 21650929 (61.24%) aligned concordantly 0 times 11668560 (33.00%) aligned concordantly exactly 1 time 2035723 (5.76%) aligned concordantly >1 times ---- 21650929 pairs aligned concordantly 0 times; of these: 3909372 (18.06%) aligned discordantly 1 time ---- 17741557 pairs aligned 0 times concordantly or discordantly; of these: 35483114 mates make up the pairs; of these: 32553957 (91.74%) aligned 0 times 1645057 (4.64%) aligned exactly 1 time 1284100 (3.62%) aligned >1 times 53.96% overall alignment rate Time searching: 01:29:00 Overall time: 01:29:00 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] 3955383 / 17514998 = 0.2258 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 14:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.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 14:18:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:03: 1000000 INFO @ Tue, 02 Aug 2022 14:19:17: 2000000 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 14:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.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 14:19:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:31: 3000000 INFO @ Tue, 02 Aug 2022 14:19:32: 1000000 INFO @ Tue, 02 Aug 2022 14:19:44: 2000000 INFO @ Tue, 02 Aug 2022 14:19:45: 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 14:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.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 14:19:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:58: 3000000 INFO @ Tue, 02 Aug 2022 14:20:01: 5000000 INFO @ Tue, 02 Aug 2022 14:20:05: 1000000 INFO @ Tue, 02 Aug 2022 14:20:13: 4000000 INFO @ Tue, 02 Aug 2022 14:20:16: 6000000 INFO @ Tue, 02 Aug 2022 14:20:20: 2000000 INFO @ Tue, 02 Aug 2022 14:20:28: 5000000 INFO @ Tue, 02 Aug 2022 14:20:32: 7000000 INFO @ Tue, 02 Aug 2022 14:20:35: 3000000 INFO @ Tue, 02 Aug 2022 14:20:43: 6000000 INFO @ Tue, 02 Aug 2022 14:20:49: 8000000 INFO @ Tue, 02 Aug 2022 14:20:51: 4000000 INFO @ Tue, 02 Aug 2022 14:21:00: 7000000 INFO @ Tue, 02 Aug 2022 14:21:07: 9000000 INFO @ Tue, 02 Aug 2022 14:21:07: 5000000 INFO @ Tue, 02 Aug 2022 14:21:15: 8000000 INFO @ Tue, 02 Aug 2022 14:21:24: 6000000 INFO @ Tue, 02 Aug 2022 14:21:26: 10000000 INFO @ Tue, 02 Aug 2022 14:21:33: 9000000 INFO @ Tue, 02 Aug 2022 14:21:42: 7000000 INFO @ Tue, 02 Aug 2022 14:21:45: 11000000 INFO @ Tue, 02 Aug 2022 14:21:52: 10000000 INFO @ Tue, 02 Aug 2022 14:22:00: 8000000 INFO @ Tue, 02 Aug 2022 14:22:05: 12000000 INFO @ Tue, 02 Aug 2022 14:22:10: 11000000 INFO @ Tue, 02 Aug 2022 14:22:20: 9000000 INFO @ Tue, 02 Aug 2022 14:22:26: 13000000 INFO @ Tue, 02 Aug 2022 14:22:29: 12000000 INFO @ Tue, 02 Aug 2022 14:22:39: 10000000 INFO @ Tue, 02 Aug 2022 14:22:46: 14000000 INFO @ Tue, 02 Aug 2022 14:22:47: 13000000 INFO @ Tue, 02 Aug 2022 14:22:57: 11000000 INFO @ Tue, 02 Aug 2022 14:23:06: 14000000 INFO @ Tue, 02 Aug 2022 14:23:07: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:23:16: 12000000 INFO @ Tue, 02 Aug 2022 14:23:24: 15000000 INFO @ Tue, 02 Aug 2022 14:23:28: 16000000 INFO @ Tue, 02 Aug 2022 14:23:35: 13000000 INFO @ Tue, 02 Aug 2022 14:23:43: 16000000 INFO @ Tue, 02 Aug 2022 14:23:50: 17000000 INFO @ Tue, 02 Aug 2022 14:23:54: 14000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:24:01: 17000000 INFO @ Tue, 02 Aug 2022 14:24:09: 18000000 INFO @ Tue, 02 Aug 2022 14:24:12: 15000000 INFO @ Tue, 02 Aug 2022 14:24:20: 18000000 INFO @ Tue, 02 Aug 2022 14:24:30: 19000000 INFO @ Tue, 02 Aug 2022 14:24:30: 16000000 INFO @ Tue, 02 Aug 2022 14:24:38: 19000000 INFO @ Tue, 02 Aug 2022 14:24:48: 17000000 INFO @ Tue, 02 Aug 2022 14:24:50: 20000000 INFO @ Tue, 02 Aug 2022 14:24:55: 20000000 INFO @ Tue, 02 Aug 2022 14:25:05: 18000000 INFO @ Tue, 02 Aug 2022 14:25:10: 21000000 INFO @ Tue, 02 Aug 2022 14:25:12: 21000000 INFO @ Tue, 02 Aug 2022 14:25:23: 19000000 INFO @ Tue, 02 Aug 2022 14:25:30: 22000000 INFO @ Tue, 02 Aug 2022 14:25:30: 22000000 INFO @ Tue, 02 Aug 2022 14:25:41: 20000000 INFO @ Tue, 02 Aug 2022 14:25:48: 23000000 INFO @ Tue, 02 Aug 2022 14:25:50: 23000000 INFO @ Tue, 02 Aug 2022 14:25:58: 21000000 INFO @ Tue, 02 Aug 2022 14:26:05: 24000000 INFO @ Tue, 02 Aug 2022 14:26:08: 24000000 INFO @ Tue, 02 Aug 2022 14:26:16: 22000000 INFO @ Tue, 02 Aug 2022 14:26:23: 25000000 INFO @ Tue, 02 Aug 2022 14:26:27: 25000000 INFO @ Tue, 02 Aug 2022 14:26:33: 23000000 INFO @ Tue, 02 Aug 2022 14:26:41: 26000000 INFO @ Tue, 02 Aug 2022 14:26:46: 26000000 INFO @ Tue, 02 Aug 2022 14:26:50: 24000000 INFO @ Tue, 02 Aug 2022 14:26:58: 27000000 INFO @ Tue, 02 Aug 2022 14:27:04: 27000000 INFO @ Tue, 02 Aug 2022 14:27:06: 25000000 INFO @ Tue, 02 Aug 2022 14:27:15: 28000000 INFO @ Tue, 02 Aug 2022 14:27:21: 26000000 INFO @ Tue, 02 Aug 2022 14:27:22: 28000000 INFO @ Tue, 02 Aug 2022 14:27:30: 29000000 INFO @ Tue, 02 Aug 2022 14:27:35: 27000000 INFO @ Tue, 02 Aug 2022 14:27:39: 29000000 INFO @ Tue, 02 Aug 2022 14:27:44: 30000000 INFO @ Tue, 02 Aug 2022 14:27:48: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:27:48: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:27:48: #1 total tags in treatment: 10493433 INFO @ Tue, 02 Aug 2022 14:27:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:48: #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 14:27:48: #1 tags after filtering in treatment: 6691794 INFO @ Tue, 02 Aug 2022 14:27:48: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 14:27:48: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:49: #2 number of paired peaks: 4664 INFO @ Tue, 02 Aug 2022 14:27:49: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:49: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:49: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:49: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:49: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 14:27:49: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 14:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.10_model.r WARNING @ Tue, 02 Aug 2022 14:27:49: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:27:49: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 14:27:49: #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 14:27:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:49: 28000000 INFO @ Tue, 02 Aug 2022 14:27:55: 30000000 INFO @ Tue, 02 Aug 2022 14:27:59: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:27:59: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:27:59: #1 total tags in treatment: 10493433 INFO @ Tue, 02 Aug 2022 14:27:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:59: #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 14:28:00: #1 tags after filtering in treatment: 6691794 INFO @ Tue, 02 Aug 2022 14:28:00: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 14:28:00: #1 finished! INFO @ Tue, 02 Aug 2022 14:28:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:28:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:28:00: #2 number of paired peaks: 4664 INFO @ Tue, 02 Aug 2022 14:28:00: start model_add_line... INFO @ Tue, 02 Aug 2022 14:28:00: start X-correlation... INFO @ Tue, 02 Aug 2022 14:28:00: end of X-cor INFO @ Tue, 02 Aug 2022 14:28:00: #2 finished! INFO @ Tue, 02 Aug 2022 14:28:00: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 14:28:00: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 14:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.05_model.r WARNING @ Tue, 02 Aug 2022 14:28:01: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:28:01: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 14:28:01: #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 14:28:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:28:01: 29000000 INFO @ Tue, 02 Aug 2022 14:28:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:28:13: 30000000 INFO @ Tue, 02 Aug 2022 14:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.10_summits.bed INFO @ Tue, 02 Aug 2022 14:28:15: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (6413 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:28:16: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:28:16: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:28:16: #1 total tags in treatment: 10493433 INFO @ Tue, 02 Aug 2022 14:28:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:28:16: #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 14:28:16: #1 tags after filtering in treatment: 6691794 INFO @ Tue, 02 Aug 2022 14:28:16: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 14:28:16: #1 finished! INFO @ Tue, 02 Aug 2022 14:28:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:28:17: #2 number of paired peaks: 4664 INFO @ Tue, 02 Aug 2022 14:28:17: start model_add_line... INFO @ Tue, 02 Aug 2022 14:28:17: start X-correlation... INFO @ Tue, 02 Aug 2022 14:28:17: end of X-cor INFO @ Tue, 02 Aug 2022 14:28:17: #2 finished! INFO @ Tue, 02 Aug 2022 14:28:17: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 14:28:17: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 14:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.20_model.r WARNING @ Tue, 02 Aug 2022 14:28:17: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:28:17: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 14:28:17: #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 14:28:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:28:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.05_summits.bed INFO @ Tue, 02 Aug 2022 14:28:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8765 records, 4 fields): 1185 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:28:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119063/SRX12119063.20_summits.bed INFO @ Tue, 02 Aug 2022 14:28:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3794 records, 4 fields): 31 millis CompletedMACS2peakCalling