Job ID = 16439874 SRX = SRX12175820 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30313663 spots for SRR15884959/SRR15884959.sra Written 30313663 spots for SRR15884959/SRR15884959.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440203 ("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: 00:54:29 30313663 reads; of these: 30313663 (100.00%) were paired; of these: 16195908 (53.43%) aligned concordantly 0 times 12283772 (40.52%) aligned concordantly exactly 1 time 1833983 (6.05%) aligned concordantly >1 times ---- 16195908 pairs aligned concordantly 0 times; of these: 2731792 (16.87%) aligned discordantly 1 time ---- 13464116 pairs aligned 0 times concordantly or discordantly; of these: 26928232 mates make up the pairs; of these: 25448128 (94.50%) aligned 0 times 695967 (2.58%) aligned exactly 1 time 784137 (2.91%) aligned >1 times 58.03% overall alignment rate Time searching: 00:54:29 Overall time: 00:54:29 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] 3453939 / 16772036 = 0.2059 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 17:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.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 17:40:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:40:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:40:35: 1000000 INFO @ Tue, 02 Aug 2022 17:40:43: 2000000 INFO @ Tue, 02 Aug 2022 17:40:51: 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 17:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.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 17:40:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:40:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:40:59: 4000000 INFO @ Tue, 02 Aug 2022 17:41:04: 1000000 INFO @ Tue, 02 Aug 2022 17:41:08: 5000000 INFO @ Tue, 02 Aug 2022 17:41:11: 2000000 INFO @ Tue, 02 Aug 2022 17:41:16: 6000000 INFO @ Tue, 02 Aug 2022 17:41:18: 3000000 INFO @ Tue, 02 Aug 2022 17:41:24: 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 17:41:25: 4000000 INFO @ Tue, 02 Aug 2022 17:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.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 17:41:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:41:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:41:32: 5000000 INFO @ Tue, 02 Aug 2022 17:41:32: 8000000 INFO @ Tue, 02 Aug 2022 17:41:34: 1000000 INFO @ Tue, 02 Aug 2022 17:41:39: 6000000 INFO @ Tue, 02 Aug 2022 17:41:41: 9000000 INFO @ Tue, 02 Aug 2022 17:41:41: 2000000 INFO @ Tue, 02 Aug 2022 17:41:46: 7000000 INFO @ Tue, 02 Aug 2022 17:41:48: 3000000 INFO @ Tue, 02 Aug 2022 17:41:49: 10000000 INFO @ Tue, 02 Aug 2022 17:41:53: 8000000 INFO @ Tue, 02 Aug 2022 17:41:55: 4000000 INFO @ Tue, 02 Aug 2022 17:41:57: 11000000 INFO @ Tue, 02 Aug 2022 17:42:01: 9000000 INFO @ Tue, 02 Aug 2022 17:42:03: 5000000 INFO @ Tue, 02 Aug 2022 17:42:06: 12000000 INFO @ Tue, 02 Aug 2022 17:42:08: 10000000 INFO @ Tue, 02 Aug 2022 17:42:10: 6000000 INFO @ Tue, 02 Aug 2022 17:42:14: 13000000 INFO @ Tue, 02 Aug 2022 17:42:15: 11000000 INFO @ Tue, 02 Aug 2022 17:42:17: 7000000 INFO @ Tue, 02 Aug 2022 17:42:22: 12000000 INFO @ Tue, 02 Aug 2022 17:42:22: 14000000 INFO @ Tue, 02 Aug 2022 17:42:24: 8000000 INFO @ Tue, 02 Aug 2022 17:42:29: 13000000 INFO @ Tue, 02 Aug 2022 17:42:30: 15000000 INFO @ Tue, 02 Aug 2022 17:42:31: 9000000 INFO @ Tue, 02 Aug 2022 17:42:36: 14000000 INFO @ Tue, 02 Aug 2022 17:42:38: 10000000 INFO @ Tue, 02 Aug 2022 17:42:39: 16000000 INFO @ Tue, 02 Aug 2022 17:42:43: 15000000 INFO @ Tue, 02 Aug 2022 17:42:45: 11000000 INFO @ Tue, 02 Aug 2022 17:42:47: 17000000 INFO @ Tue, 02 Aug 2022 17:42:50: 16000000 INFO @ Tue, 02 Aug 2022 17:42:52: 12000000 INFO @ Tue, 02 Aug 2022 17:42:55: 18000000 INFO @ Tue, 02 Aug 2022 17:42:58: 17000000 INFO @ Tue, 02 Aug 2022 17:43:00: 13000000 INFO @ Tue, 02 Aug 2022 17:43:03: 19000000 INFO @ Tue, 02 Aug 2022 17:43:05: 18000000 INFO @ Tue, 02 Aug 2022 17:43:07: 14000000 INFO @ Tue, 02 Aug 2022 17:43:12: 19000000 INFO @ Tue, 02 Aug 2022 17:43:12: 20000000 INFO @ Tue, 02 Aug 2022 17:43:14: 15000000 INFO @ Tue, 02 Aug 2022 17:43:19: 20000000 INFO @ Tue, 02 Aug 2022 17:43:20: 21000000 INFO @ Tue, 02 Aug 2022 17:43:21: 16000000 INFO @ Tue, 02 Aug 2022 17:43:26: 21000000 INFO @ Tue, 02 Aug 2022 17:43:28: 22000000 INFO @ Tue, 02 Aug 2022 17:43:28: 17000000 INFO @ Tue, 02 Aug 2022 17:43:33: 22000000 INFO @ Tue, 02 Aug 2022 17:43:35: 18000000 INFO @ Tue, 02 Aug 2022 17:43:36: 23000000 INFO @ Tue, 02 Aug 2022 17:43:40: 23000000 INFO @ Tue, 02 Aug 2022 17:43:42: 19000000 INFO @ Tue, 02 Aug 2022 17:43:45: 24000000 INFO @ Tue, 02 Aug 2022 17:43:47: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:43:50: 20000000 INFO @ Tue, 02 Aug 2022 17:43:53: 25000000 INFO @ Tue, 02 Aug 2022 17:43:55: 25000000 INFO @ Tue, 02 Aug 2022 17:43:57: 21000000 INFO @ Tue, 02 Aug 2022 17:44:02: 26000000 INFO @ Tue, 02 Aug 2022 17:44:03: 26000000 INFO @ Tue, 02 Aug 2022 17:44:04: 22000000 INFO @ Tue, 02 Aug 2022 17:44:10: 27000000 INFO @ Tue, 02 Aug 2022 17:44:11: 23000000 INFO @ Tue, 02 Aug 2022 17:44:11: 27000000 INFO @ Tue, 02 Aug 2022 17:44:18: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:44:18: 28000000 INFO @ Tue, 02 Aug 2022 17:44:19: 28000000 INFO @ Tue, 02 Aug 2022 17:44:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:44:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:44:21: #1 total tags in treatment: 11164709 INFO @ Tue, 02 Aug 2022 17:44:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:44:21: #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 17:44:21: #1 tags after filtering in treatment: 6953209 INFO @ Tue, 02 Aug 2022 17:44:21: #1 Redundant rate of treatment: 0.38 INFO @ Tue, 02 Aug 2022 17:44:21: #1 finished! INFO @ Tue, 02 Aug 2022 17:44:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:44:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:44:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:44:21: #1 total tags in treatment: 11164709 INFO @ Tue, 02 Aug 2022 17:44:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:44:21: #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 17:44:21: #1 tags after filtering in treatment: 6953209 INFO @ Tue, 02 Aug 2022 17:44:21: #1 Redundant rate of treatment: 0.38 INFO @ Tue, 02 Aug 2022 17:44:21: #1 finished! INFO @ Tue, 02 Aug 2022 17:44:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:44:21: #2 number of paired peaks: 5729 INFO @ Tue, 02 Aug 2022 17:44:21: start model_add_line... INFO @ Tue, 02 Aug 2022 17:44:22: start X-correlation... INFO @ Tue, 02 Aug 2022 17:44:22: end of X-cor INFO @ Tue, 02 Aug 2022 17:44:22: #2 finished! INFO @ Tue, 02 Aug 2022 17:44:22: #2 predicted fragment length is 241 bps INFO @ Tue, 02 Aug 2022 17:44:22: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 02 Aug 2022 17:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.05_model.r WARNING @ Tue, 02 Aug 2022 17:44:22: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:44:22: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Tue, 02 Aug 2022 17:44:22: #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 17:44:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:44:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:44:22: #2 number of paired peaks: 5729 INFO @ Tue, 02 Aug 2022 17:44:22: start model_add_line... INFO @ Tue, 02 Aug 2022 17:44:22: start X-correlation... INFO @ Tue, 02 Aug 2022 17:44:22: end of X-cor INFO @ Tue, 02 Aug 2022 17:44:22: #2 finished! INFO @ Tue, 02 Aug 2022 17:44:22: #2 predicted fragment length is 241 bps INFO @ Tue, 02 Aug 2022 17:44:22: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 02 Aug 2022 17:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.10_model.r WARNING @ Tue, 02 Aug 2022 17:44:22: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:44:22: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Tue, 02 Aug 2022 17:44:22: #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 17:44:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:44:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:44:25: 25000000 INFO @ Tue, 02 Aug 2022 17:44:32: 26000000 INFO @ Tue, 02 Aug 2022 17:44:38: 27000000 INFO @ Tue, 02 Aug 2022 17:44:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:44:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:44:45: 28000000 INFO @ Tue, 02 Aug 2022 17:44:46: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:44:46: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:44:46: #1 total tags in treatment: 11164709 INFO @ Tue, 02 Aug 2022 17:44:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:44:46: #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 17:44:47: #1 tags after filtering in treatment: 6953209 INFO @ Tue, 02 Aug 2022 17:44:47: #1 Redundant rate of treatment: 0.38 INFO @ Tue, 02 Aug 2022 17:44:47: #1 finished! INFO @ Tue, 02 Aug 2022 17:44:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:44:47: #2 number of paired peaks: 5729 INFO @ Tue, 02 Aug 2022 17:44:47: start model_add_line... INFO @ Tue, 02 Aug 2022 17:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:44:48: start X-correlation... INFO @ Tue, 02 Aug 2022 17:44:48: end of X-cor INFO @ Tue, 02 Aug 2022 17:44:48: #2 finished! INFO @ Tue, 02 Aug 2022 17:44:48: #2 predicted fragment length is 241 bps INFO @ Tue, 02 Aug 2022 17:44:48: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 02 Aug 2022 17:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.20_model.r INFO @ Tue, 02 Aug 2022 17:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.05_peaks.narrowPeak WARNING @ Tue, 02 Aug 2022 17:44:48: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:44:48: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Tue, 02 Aug 2022 17:44:48: #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 17:44:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.05_summits.bed INFO @ Tue, 02 Aug 2022 17:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.10_summits.bed INFO @ Tue, 02 Aug 2022 17:44:48: Done! INFO @ Tue, 02 Aug 2022 17:44:48: Done! pass1 - making usageList (15 chroms): 2 millis pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7535 records, 4 fields): 48 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (10279 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:45:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:45:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:45:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:45:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175820/SRX12175820.20_summits.bed INFO @ Tue, 02 Aug 2022 17:45:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4412 records, 4 fields): 20 millis CompletedMACS2peakCalling