Job ID = 12265210 SRX = SRX3945500 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17266077 spots for SRR7013050/SRR7013050.sra Written 17266077 spots for SRR7013050/SRR7013050.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265460 ("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: 00:26:09 17266077 reads; of these: 17266077 (100.00%) were paired; of these: 1917744 (11.11%) aligned concordantly 0 times 12410801 (71.88%) aligned concordantly exactly 1 time 2937532 (17.01%) aligned concordantly >1 times ---- 1917744 pairs aligned concordantly 0 times; of these: 969068 (50.53%) aligned discordantly 1 time ---- 948676 pairs aligned 0 times concordantly or discordantly; of these: 1897352 mates make up the pairs; of these: 1332826 (70.25%) aligned 0 times 285896 (15.07%) aligned exactly 1 time 278630 (14.69%) aligned >1 times 96.14% overall alignment rate Time searching: 00:26:09 Overall time: 00:26:09 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 16 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] 1228526 / 13880776 = 0.0885 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.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 @ Sat, 03 Apr 2021 06:52:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:52:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:52:56: 1000000 INFO @ Sat, 03 Apr 2021 06:53:01: 2000000 INFO @ Sat, 03 Apr 2021 06:53:07: 3000000 INFO @ Sat, 03 Apr 2021 06:53:12: 4000000 INFO @ Sat, 03 Apr 2021 06:53:17: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:53:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.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 @ Sat, 03 Apr 2021 06:53:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:53:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:53:23: 6000000 INFO @ Sat, 03 Apr 2021 06:53:26: 1000000 INFO @ Sat, 03 Apr 2021 06:53:29: 7000000 INFO @ Sat, 03 Apr 2021 06:53:33: 2000000 INFO @ Sat, 03 Apr 2021 06:53:34: 8000000 INFO @ Sat, 03 Apr 2021 06:53:39: 3000000 INFO @ Sat, 03 Apr 2021 06:53:40: 9000000 INFO @ Sat, 03 Apr 2021 06:53:45: 10000000 INFO @ Sat, 03 Apr 2021 06:53:46: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.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 @ Sat, 03 Apr 2021 06:53:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:53:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:53:51: 11000000 INFO @ Sat, 03 Apr 2021 06:53:52: 5000000 INFO @ Sat, 03 Apr 2021 06:53:56: 12000000 INFO @ Sat, 03 Apr 2021 06:53:57: 1000000 INFO @ Sat, 03 Apr 2021 06:53:59: 6000000 INFO @ Sat, 03 Apr 2021 06:54:02: 13000000 INFO @ Sat, 03 Apr 2021 06:54:03: 2000000 INFO @ Sat, 03 Apr 2021 06:54:05: 7000000 INFO @ Sat, 03 Apr 2021 06:54:08: 14000000 INFO @ Sat, 03 Apr 2021 06:54:10: 3000000 INFO @ Sat, 03 Apr 2021 06:54:11: 8000000 INFO @ Sat, 03 Apr 2021 06:54:14: 15000000 INFO @ Sat, 03 Apr 2021 06:54:16: 4000000 INFO @ Sat, 03 Apr 2021 06:54:18: 9000000 INFO @ Sat, 03 Apr 2021 06:54:20: 16000000 INFO @ Sat, 03 Apr 2021 06:54:22: 5000000 INFO @ Sat, 03 Apr 2021 06:54:24: 10000000 INFO @ Sat, 03 Apr 2021 06:54:25: 17000000 INFO @ Sat, 03 Apr 2021 06:54:29: 6000000 INFO @ Sat, 03 Apr 2021 06:54:31: 18000000 INFO @ Sat, 03 Apr 2021 06:54:31: 11000000 INFO @ Sat, 03 Apr 2021 06:54:36: 7000000 INFO @ Sat, 03 Apr 2021 06:54:36: 19000000 INFO @ Sat, 03 Apr 2021 06:54:38: 12000000 INFO @ Sat, 03 Apr 2021 06:54:42: 20000000 INFO @ Sat, 03 Apr 2021 06:54:42: 8000000 INFO @ Sat, 03 Apr 2021 06:54:45: 13000000 INFO @ Sat, 03 Apr 2021 06:54:47: 21000000 INFO @ Sat, 03 Apr 2021 06:54:48: 9000000 INFO @ Sat, 03 Apr 2021 06:54:52: 14000000 INFO @ Sat, 03 Apr 2021 06:54:53: 22000000 INFO @ Sat, 03 Apr 2021 06:54:55: 10000000 INFO @ Sat, 03 Apr 2021 06:54:58: 15000000 INFO @ Sat, 03 Apr 2021 06:54:59: 23000000 INFO @ Sat, 03 Apr 2021 06:55:02: 11000000 INFO @ Sat, 03 Apr 2021 06:55:05: 24000000 INFO @ Sat, 03 Apr 2021 06:55:05: 16000000 INFO @ Sat, 03 Apr 2021 06:55:09: 12000000 INFO @ Sat, 03 Apr 2021 06:55:10: 25000000 INFO @ Sat, 03 Apr 2021 06:55:12: 17000000 INFO @ Sat, 03 Apr 2021 06:55:16: 13000000 INFO @ Sat, 03 Apr 2021 06:55:17: 26000000 INFO @ Sat, 03 Apr 2021 06:55:19: 18000000 INFO @ Sat, 03 Apr 2021 06:55:23: 14000000 INFO @ Sat, 03 Apr 2021 06:55:23: 27000000 INFO @ Sat, 03 Apr 2021 06:55:26: 19000000 INFO @ Sat, 03 Apr 2021 06:55:29: 28000000 INFO @ Sat, 03 Apr 2021 06:55:29: 15000000 INFO @ Sat, 03 Apr 2021 06:55:32: 20000000 INFO @ Sat, 03 Apr 2021 06:55:34: 29000000 INFO @ Sat, 03 Apr 2021 06:55:36: 16000000 INFO @ Sat, 03 Apr 2021 06:55:39: 21000000 INFO @ Sat, 03 Apr 2021 06:55:39: 30000000 INFO @ Sat, 03 Apr 2021 06:55:43: 17000000 INFO @ Sat, 03 Apr 2021 06:55:44: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:55:44: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:55:44: #1 total tags in treatment: 14134984 INFO @ Sat, 03 Apr 2021 06:55:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:55:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:55:44: #1 tags after filtering in treatment: 10497523 INFO @ Sat, 03 Apr 2021 06:55:44: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:55:44: #1 finished! INFO @ Sat, 03 Apr 2021 06:55:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:55:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:55:45: #2 number of paired peaks: 1399 INFO @ Sat, 03 Apr 2021 06:55:45: start model_add_line... INFO @ Sat, 03 Apr 2021 06:55:45: start X-correlation... INFO @ Sat, 03 Apr 2021 06:55:45: end of X-cor INFO @ Sat, 03 Apr 2021 06:55:45: #2 finished! INFO @ Sat, 03 Apr 2021 06:55:45: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 06:55:45: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 03 Apr 2021 06:55:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.05_model.r WARNING @ Sat, 03 Apr 2021 06:55:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:55:45: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 03 Apr 2021 06:55:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:55:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:55:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:55:45: 22000000 INFO @ Sat, 03 Apr 2021 06:55:49: 18000000 INFO @ Sat, 03 Apr 2021 06:55:51: 23000000 INFO @ Sat, 03 Apr 2021 06:55:55: 19000000 INFO @ Sat, 03 Apr 2021 06:55:57: 24000000 INFO @ Sat, 03 Apr 2021 06:56:01: 20000000 INFO @ Sat, 03 Apr 2021 06:56:04: 25000000 INFO @ Sat, 03 Apr 2021 06:56:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:56:08: 21000000 INFO @ Sat, 03 Apr 2021 06:56:10: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:56:14: 22000000 INFO @ Sat, 03 Apr 2021 06:56:16: 27000000 INFO @ Sat, 03 Apr 2021 06:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.05_summits.bed INFO @ Sat, 03 Apr 2021 06:56:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (17107 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:56:20: 23000000 INFO @ Sat, 03 Apr 2021 06:56:23: 28000000 INFO @ Sat, 03 Apr 2021 06:56:26: 24000000 INFO @ Sat, 03 Apr 2021 06:56:29: 29000000 INFO @ Sat, 03 Apr 2021 06:56:32: 25000000 INFO @ Sat, 03 Apr 2021 06:56:35: 30000000 INFO @ Sat, 03 Apr 2021 06:56:38: 26000000 INFO @ Sat, 03 Apr 2021 06:56:40: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:56:40: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:56:40: #1 total tags in treatment: 14134984 INFO @ Sat, 03 Apr 2021 06:56:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:56:40: #1 tags after filtering in treatment: 10497523 INFO @ Sat, 03 Apr 2021 06:56:40: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:56:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:56:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:56:41: #2 number of paired peaks: 1399 INFO @ Sat, 03 Apr 2021 06:56:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:56:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:56:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:56:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:56:41: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 06:56:41: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 03 Apr 2021 06:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.10_model.r WARNING @ Sat, 03 Apr 2021 06:56:41: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:56:41: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 03 Apr 2021 06:56:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:56:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:56:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:56:44: 27000000 INFO @ Sat, 03 Apr 2021 06:56:50: 28000000 INFO @ Sat, 03 Apr 2021 06:56:56: 29000000 INFO @ Sat, 03 Apr 2021 06:57:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:57:03: 30000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:57:07: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:57:07: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:57:07: #1 total tags in treatment: 14134984 INFO @ Sat, 03 Apr 2021 06:57:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:57:08: #1 tags after filtering in treatment: 10497523 INFO @ Sat, 03 Apr 2021 06:57:08: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:57:08: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:09: #2 number of paired peaks: 1399 INFO @ Sat, 03 Apr 2021 06:57:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:09: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 06:57:09: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 03 Apr 2021 06:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.20_model.r WARNING @ Sat, 03 Apr 2021 06:57:09: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:09: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 03 Apr 2021 06:57:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:57:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:57:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:57:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.10_summits.bed INFO @ Sat, 03 Apr 2021 06:57:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8148 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:57:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3945500/SRX3945500.20_summits.bed INFO @ Sat, 03 Apr 2021 06:57:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1186 records, 4 fields): 4 millis CompletedMACS2peakCalling