Job ID = 14171367 SRX = SRX9304586 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 44658329 spots for SRR12837083/SRR12837083.sra Written 44658329 spots for SRR12837083/SRR12837083.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172020 ("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: 00:38:31 44658329 reads; of these: 44658329 (100.00%) were paired; of these: 15124392 (33.87%) aligned concordantly 0 times 25832615 (57.85%) aligned concordantly exactly 1 time 3701322 (8.29%) aligned concordantly >1 times ---- 15124392 pairs aligned concordantly 0 times; of these: 425238 (2.81%) aligned discordantly 1 time ---- 14699154 pairs aligned 0 times concordantly or discordantly; of these: 29398308 mates make up the pairs; of these: 28519452 (97.01%) aligned 0 times 669551 (2.28%) aligned exactly 1 time 209305 (0.71%) aligned >1 times 68.07% overall alignment rate Time searching: 00:38:31 Overall time: 00:38:31 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] 14328174 / 20212699 = 0.7089 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.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, 11 Dec 2021 12:21:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:21:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:21:52: 1000000 INFO @ Sat, 11 Dec 2021 12:21:56: 2000000 INFO @ Sat, 11 Dec 2021 12:22:01: 3000000 INFO @ Sat, 11 Dec 2021 12:22:06: 4000000 INFO @ Sat, 11 Dec 2021 12:22:10: 5000000 INFO @ Sat, 11 Dec 2021 12:22:15: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.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, 11 Dec 2021 12:22:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:22:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:22:20: 7000000 INFO @ Sat, 11 Dec 2021 12:22:23: 1000000 INFO @ Sat, 11 Dec 2021 12:22:25: 8000000 INFO @ Sat, 11 Dec 2021 12:22:29: 2000000 INFO @ Sat, 11 Dec 2021 12:22:30: 9000000 INFO @ Sat, 11 Dec 2021 12:22:34: 3000000 INFO @ Sat, 11 Dec 2021 12:22:35: 10000000 INFO @ Sat, 11 Dec 2021 12:22:40: 11000000 INFO @ Sat, 11 Dec 2021 12:22:40: 4000000 INFO @ Sat, 11 Dec 2021 12:22:45: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 12:22:46: 5000000 INFO @ Sat, 11 Dec 2021 12:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.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, 11 Dec 2021 12:22:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:22:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:22:50: 13000000 INFO @ Sat, 11 Dec 2021 12:22:52: 6000000 INFO @ Sat, 11 Dec 2021 12:22:52: 1000000 INFO @ Sat, 11 Dec 2021 12:22:55: 14000000 INFO @ Sat, 11 Dec 2021 12:22:57: 2000000 INFO @ Sat, 11 Dec 2021 12:22:58: 7000000 INFO @ Sat, 11 Dec 2021 12:23:00: 15000000 INFO @ Sat, 11 Dec 2021 12:23:02: 3000000 INFO @ Sat, 11 Dec 2021 12:23:04: 8000000 INFO @ Sat, 11 Dec 2021 12:23:05: 16000000 INFO @ Sat, 11 Dec 2021 12:23:08: 4000000 INFO @ Sat, 11 Dec 2021 12:23:10: 9000000 INFO @ Sat, 11 Dec 2021 12:23:10: 17000000 INFO @ Sat, 11 Dec 2021 12:23:13: 5000000 INFO @ Sat, 11 Dec 2021 12:23:15: 18000000 INFO @ Sat, 11 Dec 2021 12:23:16: 10000000 INFO @ Sat, 11 Dec 2021 12:23:18: 6000000 INFO @ Sat, 11 Dec 2021 12:23:21: 19000000 INFO @ Sat, 11 Dec 2021 12:23:22: 11000000 INFO @ Sat, 11 Dec 2021 12:23:23: 7000000 INFO @ Sat, 11 Dec 2021 12:23:26: 20000000 INFO @ Sat, 11 Dec 2021 12:23:28: 12000000 INFO @ Sat, 11 Dec 2021 12:23:28: 8000000 INFO @ Sat, 11 Dec 2021 12:23:31: 21000000 INFO @ Sat, 11 Dec 2021 12:23:33: 9000000 INFO @ Sat, 11 Dec 2021 12:23:34: 13000000 INFO @ Sat, 11 Dec 2021 12:23:36: 22000000 INFO @ Sat, 11 Dec 2021 12:23:38: 10000000 INFO @ Sat, 11 Dec 2021 12:23:40: 14000000 INFO @ Sat, 11 Dec 2021 12:23:41: 23000000 INFO @ Sat, 11 Dec 2021 12:23:43: 11000000 INFO @ Sat, 11 Dec 2021 12:23:45: 15000000 INFO @ Sat, 11 Dec 2021 12:23:46: 24000000 INFO @ Sat, 11 Dec 2021 12:23:48: 12000000 INFO @ Sat, 11 Dec 2021 12:23:51: 25000000 INFO @ Sat, 11 Dec 2021 12:23:51: 16000000 INFO @ Sat, 11 Dec 2021 12:23:54: 13000000 INFO @ Sat, 11 Dec 2021 12:23:57: 26000000 INFO @ Sat, 11 Dec 2021 12:23:57: 17000000 INFO @ Sat, 11 Dec 2021 12:23:59: 14000000 INFO @ Sat, 11 Dec 2021 12:24:02: 27000000 INFO @ Sat, 11 Dec 2021 12:24:03: 18000000 INFO @ Sat, 11 Dec 2021 12:24:04: 15000000 INFO @ Sat, 11 Dec 2021 12:24:08: 28000000 INFO @ Sat, 11 Dec 2021 12:24:09: 19000000 INFO @ Sat, 11 Dec 2021 12:24:09: 16000000 INFO @ Sat, 11 Dec 2021 12:24:13: 29000000 INFO @ Sat, 11 Dec 2021 12:24:15: 17000000 INFO @ Sat, 11 Dec 2021 12:24:15: 20000000 INFO @ Sat, 11 Dec 2021 12:24:18: 30000000 INFO @ Sat, 11 Dec 2021 12:24:20: 18000000 INFO @ Sat, 11 Dec 2021 12:24:21: 21000000 INFO @ Sat, 11 Dec 2021 12:24:23: 31000000 INFO @ Sat, 11 Dec 2021 12:24:25: 19000000 INFO @ Sat, 11 Dec 2021 12:24:27: 22000000 INFO @ Sat, 11 Dec 2021 12:24:28: 32000000 INFO @ Sat, 11 Dec 2021 12:24:29: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 12:24:29: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 12:24:29: #1 total tags in treatment: 15293448 INFO @ Sat, 11 Dec 2021 12:24:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:24:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:24:30: #1 tags after filtering in treatment: 5870087 INFO @ Sat, 11 Dec 2021 12:24:30: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 11 Dec 2021 12:24:30: #1 finished! INFO @ Sat, 11 Dec 2021 12:24:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:24:30: 20000000 INFO @ Sat, 11 Dec 2021 12:24:30: #2 number of paired peaks: 5366 INFO @ Sat, 11 Dec 2021 12:24:30: start model_add_line... INFO @ Sat, 11 Dec 2021 12:24:30: start X-correlation... INFO @ Sat, 11 Dec 2021 12:24:30: end of X-cor INFO @ Sat, 11 Dec 2021 12:24:30: #2 finished! INFO @ Sat, 11 Dec 2021 12:24:30: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 12:24:30: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 12:24:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.05_model.r WARNING @ Sat, 11 Dec 2021 12:24:30: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:24:30: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 12:24:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:24:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:24:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:24:33: 23000000 INFO @ Sat, 11 Dec 2021 12:24:35: 21000000 INFO @ Sat, 11 Dec 2021 12:24:39: 24000000 INFO @ Sat, 11 Dec 2021 12:24:40: 22000000 INFO @ Sat, 11 Dec 2021 12:24:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:24:45: 25000000 INFO @ Sat, 11 Dec 2021 12:24:45: 23000000 INFO @ Sat, 11 Dec 2021 12:24:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:24:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:24:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.05_summits.bed INFO @ Sat, 11 Dec 2021 12:24:48: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (17544 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:24:50: 24000000 INFO @ Sat, 11 Dec 2021 12:24:51: 26000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:24:56: 25000000 INFO @ Sat, 11 Dec 2021 12:24:57: 27000000 INFO @ Sat, 11 Dec 2021 12:25:01: 26000000 INFO @ Sat, 11 Dec 2021 12:25:03: 28000000 INFO @ Sat, 11 Dec 2021 12:25:06: 27000000 INFO @ Sat, 11 Dec 2021 12:25:08: 29000000 INFO @ Sat, 11 Dec 2021 12:25:11: 28000000 INFO @ Sat, 11 Dec 2021 12:25:14: 30000000 INFO @ Sat, 11 Dec 2021 12:25:16: 29000000 INFO @ Sat, 11 Dec 2021 12:25:20: 31000000 INFO @ Sat, 11 Dec 2021 12:25:21: 30000000 INFO @ Sat, 11 Dec 2021 12:25:26: 32000000 INFO @ Sat, 11 Dec 2021 12:25:26: 31000000 INFO @ Sat, 11 Dec 2021 12:25:27: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 12:25:27: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 12:25:27: #1 total tags in treatment: 15293448 INFO @ Sat, 11 Dec 2021 12:25:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:25:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:25:27: #1 tags after filtering in treatment: 5870087 INFO @ Sat, 11 Dec 2021 12:25:27: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 11 Dec 2021 12:25:27: #1 finished! INFO @ Sat, 11 Dec 2021 12:25:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:25:28: #2 number of paired peaks: 5366 INFO @ Sat, 11 Dec 2021 12:25:28: start model_add_line... INFO @ Sat, 11 Dec 2021 12:25:28: start X-correlation... INFO @ Sat, 11 Dec 2021 12:25:28: end of X-cor INFO @ Sat, 11 Dec 2021 12:25:28: #2 finished! INFO @ Sat, 11 Dec 2021 12:25:28: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 12:25:28: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 12:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.10_model.r WARNING @ Sat, 11 Dec 2021 12:25:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:25:28: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 12:25:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:25:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:25:31: 32000000 INFO @ Sat, 11 Dec 2021 12:25:32: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 12:25:32: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 12:25:32: #1 total tags in treatment: 15293448 INFO @ Sat, 11 Dec 2021 12:25:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 12:25:32: #1 tags after filtering in treatment: 5870087 INFO @ Sat, 11 Dec 2021 12:25:32: #1 Redundant rate of treatment: 0.62 INFO @ Sat, 11 Dec 2021 12:25:32: #1 finished! INFO @ Sat, 11 Dec 2021 12:25:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:25:33: #2 number of paired peaks: 5366 INFO @ Sat, 11 Dec 2021 12:25:33: start model_add_line... INFO @ Sat, 11 Dec 2021 12:25:33: start X-correlation... INFO @ Sat, 11 Dec 2021 12:25:33: end of X-cor INFO @ Sat, 11 Dec 2021 12:25:33: #2 finished! INFO @ Sat, 11 Dec 2021 12:25:33: #2 predicted fragment length is 73 bps INFO @ Sat, 11 Dec 2021 12:25:33: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 11 Dec 2021 12:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.20_model.r WARNING @ Sat, 11 Dec 2021 12:25:33: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:25:33: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 11 Dec 2021 12:25:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 12:25:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:25:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:25:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:25:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.10_summits.bed INFO @ Sat, 11 Dec 2021 12:25:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10078 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304586/SRX9304586.20_summits.bed INFO @ Sat, 11 Dec 2021 12:25:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2961 records, 4 fields): 4 millis CompletedMACS2peakCalling