Job ID = 16439864 SRX = SRX12175817 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25308930 spots for SRR15884956/SRR15884956.sra Written 25308930 spots for SRR15884956/SRR15884956.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440138 ("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: 00:48:06 25308930 reads; of these: 25308930 (100.00%) were paired; of these: 14688708 (58.04%) aligned concordantly 0 times 9061429 (35.80%) aligned concordantly exactly 1 time 1558793 (6.16%) aligned concordantly >1 times ---- 14688708 pairs aligned concordantly 0 times; of these: 4286346 (29.18%) aligned discordantly 1 time ---- 10402362 pairs aligned 0 times concordantly or discordantly; of these: 20804724 mates make up the pairs; of these: 18556269 (89.19%) aligned 0 times 1143325 (5.50%) aligned exactly 1 time 1105130 (5.31%) aligned >1 times 63.34% overall alignment rate Time searching: 00:48:06 Overall time: 00:48:06 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] 2642647 / 14849819 = 0.1780 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 17:30:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.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 17:30:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:30:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:30:46: 1000000 INFO @ Tue, 02 Aug 2022 17:30:54: 2000000 INFO @ Tue, 02 Aug 2022 17:31:02: 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 17:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.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 17:31:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:31:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:31:10: 4000000 INFO @ Tue, 02 Aug 2022 17:31:15: 1000000 INFO @ Tue, 02 Aug 2022 17:31:18: 5000000 INFO @ Tue, 02 Aug 2022 17:31:22: 2000000 INFO @ Tue, 02 Aug 2022 17:31:27: 6000000 INFO @ Tue, 02 Aug 2022 17:31:29: 3000000 INFO @ Tue, 02 Aug 2022 17:31:35: 7000000 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 17:31:37: 4000000 INFO @ Tue, 02 Aug 2022 17:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.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 17:31:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:31:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:31:43: 8000000 INFO @ Tue, 02 Aug 2022 17:31:44: 5000000 INFO @ Tue, 02 Aug 2022 17:31:46: 1000000 INFO @ Tue, 02 Aug 2022 17:31:51: 6000000 INFO @ Tue, 02 Aug 2022 17:31:52: 9000000 INFO @ Tue, 02 Aug 2022 17:31:54: 2000000 INFO @ Tue, 02 Aug 2022 17:31:59: 7000000 INFO @ Tue, 02 Aug 2022 17:32:00: 10000000 INFO @ Tue, 02 Aug 2022 17:32:03: 3000000 INFO @ Tue, 02 Aug 2022 17:32:06: 8000000 INFO @ Tue, 02 Aug 2022 17:32:09: 11000000 INFO @ Tue, 02 Aug 2022 17:32:11: 4000000 INFO @ Tue, 02 Aug 2022 17:32:13: 9000000 INFO @ Tue, 02 Aug 2022 17:32:17: 12000000 INFO @ Tue, 02 Aug 2022 17:32:20: 5000000 INFO @ Tue, 02 Aug 2022 17:32:21: 10000000 INFO @ Tue, 02 Aug 2022 17:32:26: 13000000 INFO @ Tue, 02 Aug 2022 17:32:28: 11000000 INFO @ Tue, 02 Aug 2022 17:32:28: 6000000 INFO @ Tue, 02 Aug 2022 17:32:34: 14000000 INFO @ Tue, 02 Aug 2022 17:32:36: 12000000 INFO @ Tue, 02 Aug 2022 17:32:37: 7000000 INFO @ Tue, 02 Aug 2022 17:32:43: 15000000 INFO @ Tue, 02 Aug 2022 17:32:43: 13000000 INFO @ Tue, 02 Aug 2022 17:32:45: 8000000 INFO @ Tue, 02 Aug 2022 17:32:50: 14000000 INFO @ Tue, 02 Aug 2022 17:32:51: 16000000 INFO @ Tue, 02 Aug 2022 17:32:54: 9000000 INFO @ Tue, 02 Aug 2022 17:32:58: 15000000 INFO @ Tue, 02 Aug 2022 17:33:00: 17000000 INFO @ Tue, 02 Aug 2022 17:33:02: 10000000 INFO @ Tue, 02 Aug 2022 17:33:05: 16000000 INFO @ Tue, 02 Aug 2022 17:33:09: 18000000 INFO @ Tue, 02 Aug 2022 17:33:11: 11000000 INFO @ Tue, 02 Aug 2022 17:33:13: 17000000 INFO @ Tue, 02 Aug 2022 17:33:17: 19000000 INFO @ Tue, 02 Aug 2022 17:33:20: 12000000 INFO @ Tue, 02 Aug 2022 17:33:20: 18000000 INFO @ Tue, 02 Aug 2022 17:33:26: 20000000 INFO @ Tue, 02 Aug 2022 17:33:27: 19000000 INFO @ Tue, 02 Aug 2022 17:33:28: 13000000 INFO @ Tue, 02 Aug 2022 17:33:35: 20000000 INFO @ Tue, 02 Aug 2022 17:33:35: 21000000 INFO @ Tue, 02 Aug 2022 17:33:37: 14000000 INFO @ Tue, 02 Aug 2022 17:33:42: 21000000 INFO @ Tue, 02 Aug 2022 17:33:44: 22000000 INFO @ Tue, 02 Aug 2022 17:33:45: 15000000 INFO @ Tue, 02 Aug 2022 17:33:50: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:33:53: 23000000 INFO @ Tue, 02 Aug 2022 17:33:54: 16000000 INFO @ Tue, 02 Aug 2022 17:33:58: 23000000 INFO @ Tue, 02 Aug 2022 17:34:02: 24000000 INFO @ Tue, 02 Aug 2022 17:34:03: 17000000 INFO @ Tue, 02 Aug 2022 17:34:05: 24000000 INFO @ Tue, 02 Aug 2022 17:34:11: 18000000 INFO @ Tue, 02 Aug 2022 17:34:11: 25000000 INFO @ Tue, 02 Aug 2022 17:34:13: 25000000 INFO @ Tue, 02 Aug 2022 17:34:20: 19000000 INFO @ Tue, 02 Aug 2022 17:34:20: 26000000 INFO @ Tue, 02 Aug 2022 17:34:21: 26000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:34:27: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:34:27: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:34:27: #1 total tags in treatment: 8568858 INFO @ Tue, 02 Aug 2022 17:34:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:34:27: #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 17:34:27: #1 tags after filtering in treatment: 5597868 INFO @ Tue, 02 Aug 2022 17:34:27: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 17:34:27: #1 finished! INFO @ Tue, 02 Aug 2022 17:34:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:34:28: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:34:28: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:34:28: #1 total tags in treatment: 8568858 INFO @ Tue, 02 Aug 2022 17:34:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:34:28: #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 17:34:28: #1 tags after filtering in treatment: 5597868 INFO @ Tue, 02 Aug 2022 17:34:28: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 17:34:28: #1 finished! INFO @ Tue, 02 Aug 2022 17:34:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:34:28: #2 number of paired peaks: 5159 INFO @ Tue, 02 Aug 2022 17:34:28: start model_add_line... INFO @ Tue, 02 Aug 2022 17:34:28: start X-correlation... INFO @ Tue, 02 Aug 2022 17:34:28: end of X-cor INFO @ Tue, 02 Aug 2022 17:34:28: #2 finished! INFO @ Tue, 02 Aug 2022 17:34:28: #2 predicted fragment length is 266 bps INFO @ Tue, 02 Aug 2022 17:34:28: #2 alternative fragment length(s) may be 266 bps INFO @ Tue, 02 Aug 2022 17:34:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.05_model.r WARNING @ Tue, 02 Aug 2022 17:34:28: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:34:28: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Tue, 02 Aug 2022 17:34:28: #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 17:34:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:34:28: 20000000 INFO @ Tue, 02 Aug 2022 17:34:29: #2 number of paired peaks: 5159 INFO @ Tue, 02 Aug 2022 17:34:29: start model_add_line... INFO @ Tue, 02 Aug 2022 17:34:29: start X-correlation... INFO @ Tue, 02 Aug 2022 17:34:29: end of X-cor INFO @ Tue, 02 Aug 2022 17:34:29: #2 finished! INFO @ Tue, 02 Aug 2022 17:34:29: #2 predicted fragment length is 266 bps INFO @ Tue, 02 Aug 2022 17:34:29: #2 alternative fragment length(s) may be 266 bps INFO @ Tue, 02 Aug 2022 17:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.10_model.r WARNING @ Tue, 02 Aug 2022 17:34:29: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:34:29: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Tue, 02 Aug 2022 17:34:29: #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 17:34:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:34:36: 21000000 INFO @ Tue, 02 Aug 2022 17:34:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:34:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:34:45: 22000000 INFO @ Tue, 02 Aug 2022 17:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.05_summits.bed INFO @ Tue, 02 Aug 2022 17:34:50: Done! INFO @ Tue, 02 Aug 2022 17:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:34:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.10_peaks.narrowPeak pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8940 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:34:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.10_summits.bed INFO @ Tue, 02 Aug 2022 17:34:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6191 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:34:53: 23000000 INFO @ Tue, 02 Aug 2022 17:35:01: 24000000 INFO @ Tue, 02 Aug 2022 17:35:11: 25000000 INFO @ Tue, 02 Aug 2022 17:35:20: 26000000 INFO @ Tue, 02 Aug 2022 17:35:26: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:35:26: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:35:26: #1 total tags in treatment: 8568858 INFO @ Tue, 02 Aug 2022 17:35:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:35:26: #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 17:35:27: #1 tags after filtering in treatment: 5597868 INFO @ Tue, 02 Aug 2022 17:35:27: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 17:35:27: #1 finished! INFO @ Tue, 02 Aug 2022 17:35:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:35:27: #2 number of paired peaks: 5159 INFO @ Tue, 02 Aug 2022 17:35:27: start model_add_line... INFO @ Tue, 02 Aug 2022 17:35:27: start X-correlation... INFO @ Tue, 02 Aug 2022 17:35:27: end of X-cor INFO @ Tue, 02 Aug 2022 17:35:27: #2 finished! INFO @ Tue, 02 Aug 2022 17:35:27: #2 predicted fragment length is 266 bps INFO @ Tue, 02 Aug 2022 17:35:27: #2 alternative fragment length(s) may be 266 bps INFO @ Tue, 02 Aug 2022 17:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.20_model.r WARNING @ Tue, 02 Aug 2022 17:35:27: #2 Since the d (266) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:35:27: #2 You may need to consider one of the other alternative d(s): 266 WARNING @ Tue, 02 Aug 2022 17:35:27: #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 17:35:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:35:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175817/SRX12175817.20_summits.bed INFO @ Tue, 02 Aug 2022 17:35:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3525 records, 4 fields): 60 millis CompletedMACS2peakCalling