Job ID = 14169839 SRX = SRX9910791 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33056389 spots for SRR13498862/SRR13498862.sra Written 33056389 spots for SRR13498862/SRR13498862.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170613 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:08:00 33056389 reads; of these: 33056389 (100.00%) were paired; of these: 15351595 (46.44%) aligned concordantly 0 times 7771474 (23.51%) aligned concordantly exactly 1 time 9933320 (30.05%) aligned concordantly >1 times ---- 15351595 pairs aligned concordantly 0 times; of these: 1094282 (7.13%) aligned discordantly 1 time ---- 14257313 pairs aligned 0 times concordantly or discordantly; of these: 28514626 mates make up the pairs; of these: 22688264 (79.57%) aligned 0 times 353846 (1.24%) aligned exactly 1 time 5472516 (19.19%) aligned >1 times 65.68% overall alignment rate Time searching: 01:08:01 Overall time: 01:08:01 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] 10578479 / 18642838 = 0.5674 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 04:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.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 04:53:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:53:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:53:33: 1000000 INFO @ Sat, 11 Dec 2021 04:53:44: 2000000 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 04:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.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 04:53:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:53:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:53:55: 3000000 INFO @ Sat, 11 Dec 2021 04:54:03: 1000000 INFO @ Sat, 11 Dec 2021 04:54:08: 4000000 INFO @ Sat, 11 Dec 2021 04:54:15: 2000000 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 04:54:20: 5000000 INFO @ Sat, 11 Dec 2021 04:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.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 04:54:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 04:54:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 04:54:26: 3000000 INFO @ Sat, 11 Dec 2021 04:54:33: 6000000 INFO @ Sat, 11 Dec 2021 04:54:34: 1000000 INFO @ Sat, 11 Dec 2021 04:54:38: 4000000 INFO @ Sat, 11 Dec 2021 04:54:46: 7000000 INFO @ Sat, 11 Dec 2021 04:54:47: 2000000 INFO @ Sat, 11 Dec 2021 04:54:50: 5000000 INFO @ Sat, 11 Dec 2021 04:54:59: 8000000 INFO @ Sat, 11 Dec 2021 04:55:00: 3000000 INFO @ Sat, 11 Dec 2021 04:55:02: 6000000 INFO @ Sat, 11 Dec 2021 04:55:12: 9000000 INFO @ Sat, 11 Dec 2021 04:55:13: 4000000 INFO @ Sat, 11 Dec 2021 04:55:13: 7000000 INFO @ Sat, 11 Dec 2021 04:55:24: 10000000 INFO @ Sat, 11 Dec 2021 04:55:25: 8000000 INFO @ Sat, 11 Dec 2021 04:55:26: 5000000 INFO @ Sat, 11 Dec 2021 04:55:37: 9000000 INFO @ Sat, 11 Dec 2021 04:55:37: 11000000 INFO @ Sat, 11 Dec 2021 04:55:39: 6000000 INFO @ Sat, 11 Dec 2021 04:55:48: 10000000 INFO @ Sat, 11 Dec 2021 04:55:50: 12000000 INFO @ Sat, 11 Dec 2021 04:55:51: 7000000 INFO @ Sat, 11 Dec 2021 04:56:00: 11000000 INFO @ Sat, 11 Dec 2021 04:56:03: 13000000 INFO @ Sat, 11 Dec 2021 04:56:04: 8000000 INFO @ Sat, 11 Dec 2021 04:56:11: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 04:56:15: 14000000 INFO @ Sat, 11 Dec 2021 04:56:17: 9000000 INFO @ Sat, 11 Dec 2021 04:56:23: 13000000 INFO @ Sat, 11 Dec 2021 04:56:28: 15000000 INFO @ Sat, 11 Dec 2021 04:56:30: 10000000 INFO @ Sat, 11 Dec 2021 04:56:35: 14000000 INFO @ Sat, 11 Dec 2021 04:56:41: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 04:56:43: 11000000 INFO @ Sat, 11 Dec 2021 04:56:46: 15000000 INFO @ Sat, 11 Dec 2021 04:56:54: 17000000 INFO @ Sat, 11 Dec 2021 04:56:55: 12000000 INFO @ Sat, 11 Dec 2021 04:56:58: 16000000 INFO @ Sat, 11 Dec 2021 04:57:06: 18000000 INFO @ Sat, 11 Dec 2021 04:57:08: 13000000 INFO @ Sat, 11 Dec 2021 04:57:10: 17000000 INFO @ Sat, 11 Dec 2021 04:57:19: 19000000 INFO @ Sat, 11 Dec 2021 04:57:21: 14000000 INFO @ Sat, 11 Dec 2021 04:57:21: 18000000 INFO @ Sat, 11 Dec 2021 04:57:32: 20000000 INFO @ Sat, 11 Dec 2021 04:57:33: 19000000 INFO @ Sat, 11 Dec 2021 04:57:34: 15000000 INFO @ Sat, 11 Dec 2021 04:57:45: 20000000 INFO @ Sat, 11 Dec 2021 04:57:45: 21000000 INFO @ Sat, 11 Dec 2021 04:57:47: 16000000 INFO @ Sat, 11 Dec 2021 04:57:57: 21000000 INFO @ Sat, 11 Dec 2021 04:57:58: 22000000 INFO @ Sat, 11 Dec 2021 04:57:59: 17000000 INFO @ Sat, 11 Dec 2021 04:58:01: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 04:58:01: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 04:58:01: #1 total tags in treatment: 7501086 INFO @ Sat, 11 Dec 2021 04:58:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:58:01: #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 04:58:01: #1 tags after filtering in treatment: 5795964 INFO @ Sat, 11 Dec 2021 04:58:01: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 04:58:01: #1 finished! INFO @ Sat, 11 Dec 2021 04:58:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:58:02: #2 number of paired peaks: 336 WARNING @ Sat, 11 Dec 2021 04:58:02: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sat, 11 Dec 2021 04:58:02: start model_add_line... INFO @ Sat, 11 Dec 2021 04:58:02: start X-correlation... INFO @ Sat, 11 Dec 2021 04:58:02: end of X-cor INFO @ Sat, 11 Dec 2021 04:58:02: #2 finished! INFO @ Sat, 11 Dec 2021 04:58:02: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Dec 2021 04:58:02: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 11 Dec 2021 04:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.05_model.r WARNING @ Sat, 11 Dec 2021 04:58:02: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:58:02: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 11 Dec 2021 04:58:02: #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 04:58:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:58:08: 22000000 INFO @ Sat, 11 Dec 2021 04:58:11: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 04:58:11: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 04:58:11: #1 total tags in treatment: 7501086 INFO @ Sat, 11 Dec 2021 04:58:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:58:11: #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 04:58:11: #1 tags after filtering in treatment: 5795964 INFO @ Sat, 11 Dec 2021 04:58:11: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 04:58:11: #1 finished! INFO @ Sat, 11 Dec 2021 04:58:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:58:12: #2 number of paired peaks: 336 WARNING @ Sat, 11 Dec 2021 04:58:12: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sat, 11 Dec 2021 04:58:12: start model_add_line... INFO @ Sat, 11 Dec 2021 04:58:12: 18000000 INFO @ Sat, 11 Dec 2021 04:58:12: start X-correlation... INFO @ Sat, 11 Dec 2021 04:58:12: end of X-cor INFO @ Sat, 11 Dec 2021 04:58:12: #2 finished! INFO @ Sat, 11 Dec 2021 04:58:12: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Dec 2021 04:58:12: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 11 Dec 2021 04:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.10_model.r WARNING @ Sat, 11 Dec 2021 04:58:12: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:58:12: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 11 Dec 2021 04:58:12: #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 04:58:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:58:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.05_peaks.xls INFO @ Sat, 11 Dec 2021 04:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.05_summits.bed INFO @ Sat, 11 Dec 2021 04:58:21: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2093 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 04:58:23: 19000000 INFO @ Sat, 11 Dec 2021 04:58:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.10_peaks.xls INFO @ Sat, 11 Dec 2021 04:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.10_summits.bed INFO @ Sat, 11 Dec 2021 04:58:31: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (773 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 04:58:34: 20000000 INFO @ Sat, 11 Dec 2021 04:58:45: 21000000 INFO @ Sat, 11 Dec 2021 04:58:56: 22000000 INFO @ Sat, 11 Dec 2021 04:58:59: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 04:58:59: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 04:58:59: #1 total tags in treatment: 7501086 INFO @ Sat, 11 Dec 2021 04:58:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 04:58:59: #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 04:58:59: #1 tags after filtering in treatment: 5795964 INFO @ Sat, 11 Dec 2021 04:58:59: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 04:58:59: #1 finished! INFO @ Sat, 11 Dec 2021 04:58:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 04:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 04:59:00: #2 number of paired peaks: 336 WARNING @ Sat, 11 Dec 2021 04:59:00: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sat, 11 Dec 2021 04:59:00: start model_add_line... INFO @ Sat, 11 Dec 2021 04:59:00: start X-correlation... INFO @ Sat, 11 Dec 2021 04:59:00: end of X-cor INFO @ Sat, 11 Dec 2021 04:59:00: #2 finished! INFO @ Sat, 11 Dec 2021 04:59:00: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Dec 2021 04:59:00: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 11 Dec 2021 04:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.20_model.r WARNING @ Sat, 11 Dec 2021 04:59:00: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 04:59:00: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 11 Dec 2021 04:59:00: #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 04:59:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 04:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 04:59:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 04:59:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.20_peaks.xls INFO @ Sat, 11 Dec 2021 04:59:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 04:59:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910791/SRX9910791.20_summits.bed INFO @ Sat, 11 Dec 2021 04:59:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 1 millis CompletedMACS2peakCalling