Job ID = 16437291 SRX = SRX12119064 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38217020 spots for SRR15827102/SRR15827102.sra Written 38217020 spots for SRR15827102/SRR15827102.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438100 ("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: 01:04:02 38217020 reads; of these: 38217020 (100.00%) were paired; of these: 24189565 (63.30%) aligned concordantly 0 times 11952327 (31.27%) aligned concordantly exactly 1 time 2075128 (5.43%) aligned concordantly >1 times ---- 24189565 pairs aligned concordantly 0 times; of these: 4206823 (17.39%) aligned discordantly 1 time ---- 19982742 pairs aligned 0 times concordantly or discordantly; of these: 39965484 mates make up the pairs; of these: 36838445 (92.18%) aligned 0 times 1792316 (4.48%) aligned exactly 1 time 1334723 (3.34%) aligned >1 times 51.80% overall alignment rate Time searching: 01:04:02 Overall time: 01:04:02 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 32 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] 3851567 / 18135430 = 0.2124 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 13:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.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 13:49:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:49:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:49:27: 1000000 INFO @ Tue, 02 Aug 2022 13:49:37: 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 13:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.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 13:49:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:49:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:49:48: 3000000 INFO @ Tue, 02 Aug 2022 13:49:56: 1000000 INFO @ Tue, 02 Aug 2022 13:50:00: 4000000 INFO @ Tue, 02 Aug 2022 13:50:07: 2000000 INFO @ Tue, 02 Aug 2022 13:50:12: 5000000 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 13:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.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 13:50:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:50:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:50:19: 3000000 INFO @ Tue, 02 Aug 2022 13:50:24: 6000000 INFO @ Tue, 02 Aug 2022 13:50:27: 1000000 INFO @ Tue, 02 Aug 2022 13:50:30: 4000000 INFO @ Tue, 02 Aug 2022 13:50:36: 7000000 INFO @ Tue, 02 Aug 2022 13:50:38: 2000000 INFO @ Tue, 02 Aug 2022 13:50:42: 5000000 INFO @ Tue, 02 Aug 2022 13:50:49: 8000000 INFO @ Tue, 02 Aug 2022 13:50:49: 3000000 INFO @ Tue, 02 Aug 2022 13:50:53: 6000000 INFO @ Tue, 02 Aug 2022 13:51:01: 4000000 INFO @ Tue, 02 Aug 2022 13:51:01: 9000000 INFO @ Tue, 02 Aug 2022 13:51:05: 7000000 INFO @ Tue, 02 Aug 2022 13:51:12: 5000000 INFO @ Tue, 02 Aug 2022 13:51:14: 10000000 INFO @ Tue, 02 Aug 2022 13:51:17: 8000000 INFO @ Tue, 02 Aug 2022 13:51:23: 6000000 INFO @ Tue, 02 Aug 2022 13:51:26: 11000000 INFO @ Tue, 02 Aug 2022 13:51:28: 9000000 INFO @ Tue, 02 Aug 2022 13:51:35: 7000000 INFO @ Tue, 02 Aug 2022 13:51:38: 12000000 INFO @ Tue, 02 Aug 2022 13:51:39: 10000000 INFO @ Tue, 02 Aug 2022 13:51:46: 8000000 INFO @ Tue, 02 Aug 2022 13:51:50: 11000000 INFO @ Tue, 02 Aug 2022 13:51:50: 13000000 INFO @ Tue, 02 Aug 2022 13:51:57: 9000000 INFO @ Tue, 02 Aug 2022 13:52:01: 12000000 INFO @ Tue, 02 Aug 2022 13:52:02: 14000000 INFO @ Tue, 02 Aug 2022 13:52:08: 10000000 INFO @ Tue, 02 Aug 2022 13:52:12: 13000000 INFO @ Tue, 02 Aug 2022 13:52:14: 15000000 INFO @ Tue, 02 Aug 2022 13:52:19: 11000000 INFO @ Tue, 02 Aug 2022 13:52:23: 14000000 INFO @ Tue, 02 Aug 2022 13:52:26: 16000000 INFO @ Tue, 02 Aug 2022 13:52:31: 12000000 INFO @ Tue, 02 Aug 2022 13:52:34: 15000000 INFO @ Tue, 02 Aug 2022 13:52:37: 17000000 INFO @ Tue, 02 Aug 2022 13:52:42: 13000000 INFO @ Tue, 02 Aug 2022 13:52:46: 16000000 INFO @ Tue, 02 Aug 2022 13:52:49: 18000000 INFO @ Tue, 02 Aug 2022 13:52:53: 14000000 INFO @ Tue, 02 Aug 2022 13:52:57: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:53:01: 19000000 INFO @ Tue, 02 Aug 2022 13:53:04: 15000000 INFO @ Tue, 02 Aug 2022 13:53:08: 18000000 INFO @ Tue, 02 Aug 2022 13:53:13: 20000000 INFO @ Tue, 02 Aug 2022 13:53:15: 16000000 INFO @ Tue, 02 Aug 2022 13:53:19: 19000000 INFO @ Tue, 02 Aug 2022 13:53:25: 21000000 INFO @ Tue, 02 Aug 2022 13:53:26: 17000000 INFO @ Tue, 02 Aug 2022 13:53:30: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:53:36: 22000000 INFO @ Tue, 02 Aug 2022 13:53:37: 18000000 INFO @ Tue, 02 Aug 2022 13:53:41: 21000000 INFO @ Tue, 02 Aug 2022 13:53:48: 19000000 INFO @ Tue, 02 Aug 2022 13:53:48: 23000000 INFO @ Tue, 02 Aug 2022 13:53:52: 22000000 INFO @ Tue, 02 Aug 2022 13:53:59: 20000000 INFO @ Tue, 02 Aug 2022 13:54:00: 24000000 INFO @ Tue, 02 Aug 2022 13:54:03: 23000000 INFO @ Tue, 02 Aug 2022 13:54:10: 21000000 INFO @ Tue, 02 Aug 2022 13:54:12: 25000000 INFO @ Tue, 02 Aug 2022 13:54:15: 24000000 INFO @ Tue, 02 Aug 2022 13:54:21: 22000000 INFO @ Tue, 02 Aug 2022 13:54:24: 26000000 INFO @ Tue, 02 Aug 2022 13:54:26: 25000000 INFO @ Tue, 02 Aug 2022 13:54:33: 23000000 INFO @ Tue, 02 Aug 2022 13:54:36: 27000000 INFO @ Tue, 02 Aug 2022 13:54:38: 26000000 INFO @ Tue, 02 Aug 2022 13:54:44: 24000000 INFO @ Tue, 02 Aug 2022 13:54:48: 28000000 INFO @ Tue, 02 Aug 2022 13:54:49: 27000000 INFO @ Tue, 02 Aug 2022 13:54:55: 25000000 INFO @ Tue, 02 Aug 2022 13:55:00: 29000000 INFO @ Tue, 02 Aug 2022 13:55:01: 28000000 INFO @ Tue, 02 Aug 2022 13:55:07: 26000000 INFO @ Tue, 02 Aug 2022 13:55:12: 30000000 INFO @ Tue, 02 Aug 2022 13:55:12: 29000000 INFO @ Tue, 02 Aug 2022 13:55:18: 27000000 INFO @ Tue, 02 Aug 2022 13:55:24: 30000000 INFO @ Tue, 02 Aug 2022 13:55:24: 31000000 INFO @ Tue, 02 Aug 2022 13:55:29: 28000000 INFO @ Tue, 02 Aug 2022 13:55:34: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:55:34: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:55:34: #1 total tags in treatment: 10945088 INFO @ Tue, 02 Aug 2022 13:55:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:55:34: #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 13:55:35: #1 tags after filtering in treatment: 7099851 INFO @ Tue, 02 Aug 2022 13:55:35: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 13:55:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:55:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:55:35: 31000000 INFO @ Tue, 02 Aug 2022 13:55:35: #2 number of paired peaks: 4442 INFO @ Tue, 02 Aug 2022 13:55:35: start model_add_line... INFO @ Tue, 02 Aug 2022 13:55:35: start X-correlation... INFO @ Tue, 02 Aug 2022 13:55:36: end of X-cor INFO @ Tue, 02 Aug 2022 13:55:36: #2 finished! INFO @ Tue, 02 Aug 2022 13:55:36: #2 predicted fragment length is 226 bps INFO @ Tue, 02 Aug 2022 13:55:36: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 02 Aug 2022 13:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.05_model.r WARNING @ Tue, 02 Aug 2022 13:55:36: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:55:36: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Tue, 02 Aug 2022 13:55:36: #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 13:55:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:55:40: 29000000 INFO @ Tue, 02 Aug 2022 13:55:45: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:55:45: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:55:45: #1 total tags in treatment: 10945088 INFO @ Tue, 02 Aug 2022 13:55:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:55:45: #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 13:55:45: #1 tags after filtering in treatment: 7099851 INFO @ Tue, 02 Aug 2022 13:55:45: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 13:55:45: #1 finished! INFO @ Tue, 02 Aug 2022 13:55:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:55:46: #2 number of paired peaks: 4442 INFO @ Tue, 02 Aug 2022 13:55:46: start model_add_line... INFO @ Tue, 02 Aug 2022 13:55:46: start X-correlation... INFO @ Tue, 02 Aug 2022 13:55:46: end of X-cor INFO @ Tue, 02 Aug 2022 13:55:46: #2 finished! INFO @ Tue, 02 Aug 2022 13:55:46: #2 predicted fragment length is 226 bps INFO @ Tue, 02 Aug 2022 13:55:46: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 02 Aug 2022 13:55:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.10_model.r WARNING @ Tue, 02 Aug 2022 13:55:46: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:55:46: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Tue, 02 Aug 2022 13:55:46: #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 13:55:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:55:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:55:51: 30000000 INFO @ Tue, 02 Aug 2022 13:55:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:56:00: 31000000 INFO @ Tue, 02 Aug 2022 13:56:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:56:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:56:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.05_summits.bed INFO @ Tue, 02 Aug 2022 13:56:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8708 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:56:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:56:09: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:56:09: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:56:09: #1 total tags in treatment: 10945088 INFO @ Tue, 02 Aug 2022 13:56:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:56:09: #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 13:56:09: #1 tags after filtering in treatment: 7099851 INFO @ Tue, 02 Aug 2022 13:56:09: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 02 Aug 2022 13:56:09: #1 finished! INFO @ Tue, 02 Aug 2022 13:56:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:56:10: #2 number of paired peaks: 4442 INFO @ Tue, 02 Aug 2022 13:56:10: start model_add_line... INFO @ Tue, 02 Aug 2022 13:56:10: start X-correlation... INFO @ Tue, 02 Aug 2022 13:56:10: end of X-cor INFO @ Tue, 02 Aug 2022 13:56:10: #2 finished! INFO @ Tue, 02 Aug 2022 13:56:10: #2 predicted fragment length is 226 bps INFO @ Tue, 02 Aug 2022 13:56:10: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 02 Aug 2022 13:56:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.20_model.r WARNING @ Tue, 02 Aug 2022 13:56:10: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:56:10: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Tue, 02 Aug 2022 13:56:10: #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 13:56:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:56:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.10_summits.bed INFO @ Tue, 02 Aug 2022 13:56:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6326 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:56:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12119064/SRX12119064.20_summits.bed INFO @ Tue, 02 Aug 2022 13:56:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3750 records, 4 fields): 24 millis CompletedMACS2peakCalling