Job ID = 14168821 SRX = ERX3978779 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17099206 spots for ERR3975800/ERR3975800.sra Written 17099206 spots for ERR3975800/ERR3975800.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169904 ("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: 00:36:37 17099206 reads; of these: 17099206 (100.00%) were paired; of these: 6235777 (36.47%) aligned concordantly 0 times 5375857 (31.44%) aligned concordantly exactly 1 time 5487572 (32.09%) aligned concordantly >1 times ---- 6235777 pairs aligned concordantly 0 times; of these: 1632736 (26.18%) aligned discordantly 1 time ---- 4603041 pairs aligned 0 times concordantly or discordantly; of these: 9206082 mates make up the pairs; of these: 5788731 (62.88%) aligned 0 times 326161 (3.54%) aligned exactly 1 time 3091190 (33.58%) aligned >1 times 83.07% overall alignment rate Time searching: 00:36:37 Overall time: 00:36:37 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 20 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] 3958704 / 12416990 = 0.3188 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 @ Fri, 10 Dec 2021 21:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.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 @ Fri, 10 Dec 2021 21:28:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:28:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:28:08: 1000000 INFO @ Fri, 10 Dec 2021 21:28:15: 2000000 INFO @ Fri, 10 Dec 2021 21:28:22: 3000000 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 @ Fri, 10 Dec 2021 21:28:29: 4000000 INFO @ Fri, 10 Dec 2021 21:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.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 @ Fri, 10 Dec 2021 21:28:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:28:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:28:37: 5000000 INFO @ Fri, 10 Dec 2021 21:28:39: 1000000 INFO @ Fri, 10 Dec 2021 21:28:44: 6000000 INFO @ Fri, 10 Dec 2021 21:28:47: 2000000 INFO @ Fri, 10 Dec 2021 21:28:52: 7000000 INFO @ Fri, 10 Dec 2021 21:28:54: 3000000 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 @ Fri, 10 Dec 2021 21:29:00: 8000000 INFO @ Fri, 10 Dec 2021 21:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.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 @ Fri, 10 Dec 2021 21:29:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:29:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:29:02: 4000000 INFO @ Fri, 10 Dec 2021 21:29:09: 9000000 INFO @ Fri, 10 Dec 2021 21:29:11: 1000000 INFO @ Fri, 10 Dec 2021 21:29:11: 5000000 INFO @ Fri, 10 Dec 2021 21:29:17: 10000000 INFO @ Fri, 10 Dec 2021 21:29:20: 6000000 INFO @ Fri, 10 Dec 2021 21:29:20: 2000000 INFO @ Fri, 10 Dec 2021 21:29:26: 11000000 INFO @ Fri, 10 Dec 2021 21:29:28: 7000000 INFO @ Fri, 10 Dec 2021 21:29:30: 3000000 INFO @ Fri, 10 Dec 2021 21:29:34: 12000000 INFO @ Fri, 10 Dec 2021 21:29:37: 8000000 INFO @ Fri, 10 Dec 2021 21:29:40: 4000000 INFO @ Fri, 10 Dec 2021 21:29:42: 13000000 INFO @ Fri, 10 Dec 2021 21:29:45: 9000000 INFO @ Fri, 10 Dec 2021 21:29:50: 5000000 INFO @ Fri, 10 Dec 2021 21:29:50: 14000000 INFO @ Fri, 10 Dec 2021 21:29:54: 10000000 INFO @ Fri, 10 Dec 2021 21:29:58: 15000000 INFO @ Fri, 10 Dec 2021 21:30:00: 6000000 INFO @ Fri, 10 Dec 2021 21:30:02: 11000000 INFO @ Fri, 10 Dec 2021 21:30:06: 16000000 INFO @ Fri, 10 Dec 2021 21:30:10: 7000000 INFO @ Fri, 10 Dec 2021 21:30:10: 12000000 INFO @ Fri, 10 Dec 2021 21:30:14: 17000000 INFO @ Fri, 10 Dec 2021 21:30:18: 13000000 INFO @ Fri, 10 Dec 2021 21:30:19: 8000000 INFO @ Fri, 10 Dec 2021 21:30:22: 18000000 INFO @ Fri, 10 Dec 2021 21:30:26: 14000000 INFO @ Fri, 10 Dec 2021 21:30:29: 9000000 INFO @ Fri, 10 Dec 2021 21:30:31: 19000000 INFO @ Fri, 10 Dec 2021 21:30:34: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:30:39: 10000000 INFO @ Fri, 10 Dec 2021 21:30:39: 20000000 INFO @ Fri, 10 Dec 2021 21:30:42: 16000000 INFO @ Fri, 10 Dec 2021 21:30:43: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:30:43: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:30:43: #1 total tags in treatment: 7000211 INFO @ Fri, 10 Dec 2021 21:30:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:30:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:30:43: #1 tags after filtering in treatment: 5020051 INFO @ Fri, 10 Dec 2021 21:30:43: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 21:30:43: #1 finished! INFO @ Fri, 10 Dec 2021 21:30:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:30:44: #2 number of paired peaks: 4800 INFO @ Fri, 10 Dec 2021 21:30:44: start model_add_line... INFO @ Fri, 10 Dec 2021 21:30:44: start X-correlation... INFO @ Fri, 10 Dec 2021 21:30:44: end of X-cor INFO @ Fri, 10 Dec 2021 21:30:44: #2 finished! INFO @ Fri, 10 Dec 2021 21:30:44: #2 predicted fragment length is 210 bps INFO @ Fri, 10 Dec 2021 21:30:44: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 10 Dec 2021 21:30:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.05_model.r WARNING @ Fri, 10 Dec 2021 21:30:44: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:30:44: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Fri, 10 Dec 2021 21:30:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:30:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:30:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:30:48: 11000000 INFO @ Fri, 10 Dec 2021 21:30:50: 17000000 INFO @ Fri, 10 Dec 2021 21:30:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:30:58: 12000000 INFO @ Fri, 10 Dec 2021 21:30:58: 18000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.05_summits.bed INFO @ Fri, 10 Dec 2021 21:31:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10091 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:31:07: 19000000 INFO @ Fri, 10 Dec 2021 21:31:07: 13000000 INFO @ Fri, 10 Dec 2021 21:31:15: 20000000 INFO @ Fri, 10 Dec 2021 21:31:16: 14000000 INFO @ Fri, 10 Dec 2021 21:31:19: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:31:19: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:31:19: #1 total tags in treatment: 7000211 INFO @ Fri, 10 Dec 2021 21:31:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:31:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:31:19: #1 tags after filtering in treatment: 5020051 INFO @ Fri, 10 Dec 2021 21:31:19: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 21:31:19: #1 finished! INFO @ Fri, 10 Dec 2021 21:31:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:31:20: #2 number of paired peaks: 4800 INFO @ Fri, 10 Dec 2021 21:31:20: start model_add_line... INFO @ Fri, 10 Dec 2021 21:31:20: start X-correlation... INFO @ Fri, 10 Dec 2021 21:31:20: end of X-cor INFO @ Fri, 10 Dec 2021 21:31:20: #2 finished! INFO @ Fri, 10 Dec 2021 21:31:20: #2 predicted fragment length is 210 bps INFO @ Fri, 10 Dec 2021 21:31:20: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 10 Dec 2021 21:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.10_model.r WARNING @ Fri, 10 Dec 2021 21:31:20: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:31:20: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Fri, 10 Dec 2021 21:31:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:31:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:31:25: 15000000 INFO @ Fri, 10 Dec 2021 21:31:34: 16000000 INFO @ Fri, 10 Dec 2021 21:31:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:31:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:31:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:31:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.10_summits.bed INFO @ Fri, 10 Dec 2021 21:31:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6344 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:31:42: 17000000 INFO @ Fri, 10 Dec 2021 21:31:51: 18000000 INFO @ Fri, 10 Dec 2021 21:32:00: 19000000 INFO @ Fri, 10 Dec 2021 21:32:09: 20000000 INFO @ Fri, 10 Dec 2021 21:32:14: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:32:14: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:32:14: #1 total tags in treatment: 7000211 INFO @ Fri, 10 Dec 2021 21:32:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:32:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:32:14: #1 tags after filtering in treatment: 5020051 INFO @ Fri, 10 Dec 2021 21:32:14: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 21:32:14: #1 finished! INFO @ Fri, 10 Dec 2021 21:32:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:32:14: #2 number of paired peaks: 4800 INFO @ Fri, 10 Dec 2021 21:32:14: start model_add_line... INFO @ Fri, 10 Dec 2021 21:32:14: start X-correlation... INFO @ Fri, 10 Dec 2021 21:32:14: end of X-cor INFO @ Fri, 10 Dec 2021 21:32:14: #2 finished! INFO @ Fri, 10 Dec 2021 21:32:14: #2 predicted fragment length is 210 bps INFO @ Fri, 10 Dec 2021 21:32:14: #2 alternative fragment length(s) may be 210 bps INFO @ Fri, 10 Dec 2021 21:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.20_model.r WARNING @ Fri, 10 Dec 2021 21:32:14: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:32:14: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Fri, 10 Dec 2021 21:32:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:32:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:32:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978779/ERX3978779.20_summits.bed INFO @ Fri, 10 Dec 2021 21:32:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2552 records, 4 fields): 4 millis CompletedMACS2peakCalling