Job ID = 14168396 SRX = ERX3978749 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12836506 spots for ERR3975761/ERR3975761.sra Written 12836506 spots for ERR3975761/ERR3975761.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169620 ("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: 00:23:25 12836506 reads; of these: 12836506 (100.00%) were paired; of these: 6052316 (47.15%) aligned concordantly 0 times 3330533 (25.95%) aligned concordantly exactly 1 time 3453657 (26.90%) aligned concordantly >1 times ---- 6052316 pairs aligned concordantly 0 times; of these: 942179 (15.57%) aligned discordantly 1 time ---- 5110137 pairs aligned 0 times concordantly or discordantly; of these: 10220274 mates make up the pairs; of these: 7066431 (69.14%) aligned 0 times 238702 (2.34%) aligned exactly 1 time 2915141 (28.52%) aligned >1 times 72.48% overall alignment rate Time searching: 00:23:26 Overall time: 00:23:26 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 12 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] 2457426 / 7646654 = 0.3214 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 18:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.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 18:49:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:49:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:50:04: 1000000 INFO @ Fri, 10 Dec 2021 18:50:12: 2000000 INFO @ Fri, 10 Dec 2021 18:50:19: 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 18:50:27: 4000000 INFO @ Fri, 10 Dec 2021 18:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.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 18:50:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:50:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:50:35: 1000000 INFO @ Fri, 10 Dec 2021 18:50:35: 5000000 INFO @ Fri, 10 Dec 2021 18:50:42: 2000000 INFO @ Fri, 10 Dec 2021 18:50:43: 6000000 INFO @ Fri, 10 Dec 2021 18:50:50: 3000000 INFO @ Fri, 10 Dec 2021 18:50:51: 7000000 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 18:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.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 18:50:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:50:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:50:58: 4000000 INFO @ Fri, 10 Dec 2021 18:50:59: 8000000 INFO @ Fri, 10 Dec 2021 18:51:04: 1000000 INFO @ Fri, 10 Dec 2021 18:51:06: 5000000 INFO @ Fri, 10 Dec 2021 18:51:07: 9000000 INFO @ Fri, 10 Dec 2021 18:51:11: 2000000 INFO @ Fri, 10 Dec 2021 18:51:14: 6000000 INFO @ Fri, 10 Dec 2021 18:51:15: 10000000 INFO @ Fri, 10 Dec 2021 18:51:18: 3000000 INFO @ Fri, 10 Dec 2021 18:51:22: 7000000 INFO @ Fri, 10 Dec 2021 18:51:24: 11000000 INFO @ Fri, 10 Dec 2021 18:51:25: 4000000 INFO @ Fri, 10 Dec 2021 18:51:29: 8000000 INFO @ Fri, 10 Dec 2021 18:51:32: 5000000 INFO @ Fri, 10 Dec 2021 18:51:32: 12000000 INFO @ Fri, 10 Dec 2021 18:51:37: 9000000 INFO @ Fri, 10 Dec 2021 18:51:39: 6000000 INFO @ Fri, 10 Dec 2021 18:51:40: 13000000 INFO @ Fri, 10 Dec 2021 18:51:44: 10000000 INFO @ Fri, 10 Dec 2021 18:51:46: 7000000 INFO @ Fri, 10 Dec 2021 18:51:46: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:51:46: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:51:46: #1 total tags in treatment: 4412354 INFO @ Fri, 10 Dec 2021 18:51:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:51:46: #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 18:51:46: #1 tags after filtering in treatment: 3303345 INFO @ Fri, 10 Dec 2021 18:51:46: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 18:51:46: #1 finished! INFO @ Fri, 10 Dec 2021 18:51:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:51:47: #2 number of paired peaks: 4740 INFO @ Fri, 10 Dec 2021 18:51:47: start model_add_line... INFO @ Fri, 10 Dec 2021 18:51:47: start X-correlation... INFO @ Fri, 10 Dec 2021 18:51:47: end of X-cor INFO @ Fri, 10 Dec 2021 18:51:47: #2 finished! INFO @ Fri, 10 Dec 2021 18:51:47: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 18:51:47: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 18:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.05_model.r WARNING @ Fri, 10 Dec 2021 18:51:47: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:51:47: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 18:51:47: #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 18:51:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:51:52: 11000000 INFO @ Fri, 10 Dec 2021 18:51:52: 8000000 INFO @ Fri, 10 Dec 2021 18:51:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:51:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.05_summits.bed INFO @ Fri, 10 Dec 2021 18:51:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8940 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:51:59: 9000000 INFO @ Fri, 10 Dec 2021 18:51:59: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:52:06: 10000000 INFO @ Fri, 10 Dec 2021 18:52:07: 13000000 INFO @ Fri, 10 Dec 2021 18:52:12: 11000000 INFO @ Fri, 10 Dec 2021 18:52:12: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:52:12: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:52:12: #1 total tags in treatment: 4412354 INFO @ Fri, 10 Dec 2021 18:52:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:52:12: #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 18:52:13: #1 tags after filtering in treatment: 3303345 INFO @ Fri, 10 Dec 2021 18:52:13: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 18:52:13: #1 finished! INFO @ Fri, 10 Dec 2021 18:52:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:52:13: #2 number of paired peaks: 4740 INFO @ Fri, 10 Dec 2021 18:52:13: start model_add_line... INFO @ Fri, 10 Dec 2021 18:52:13: start X-correlation... INFO @ Fri, 10 Dec 2021 18:52:13: end of X-cor INFO @ Fri, 10 Dec 2021 18:52:13: #2 finished! INFO @ Fri, 10 Dec 2021 18:52:13: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 18:52:13: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 18:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.10_model.r WARNING @ Fri, 10 Dec 2021 18:52:13: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:52:13: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 18:52:13: #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 18:52:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:52:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:52:18: 12000000 INFO @ Fri, 10 Dec 2021 18:52:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:52:25: 13000000 INFO @ Fri, 10 Dec 2021 18:52:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:52:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:52:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.10_summits.bed INFO @ Fri, 10 Dec 2021 18:52:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4753 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:52:29: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:52:29: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:52:29: #1 total tags in treatment: 4412354 INFO @ Fri, 10 Dec 2021 18:52:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:52:29: #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 18:52:30: #1 tags after filtering in treatment: 3303345 INFO @ Fri, 10 Dec 2021 18:52:30: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 18:52:30: #1 finished! INFO @ Fri, 10 Dec 2021 18:52:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:52:30: #2 number of paired peaks: 4740 INFO @ Fri, 10 Dec 2021 18:52:30: start model_add_line... INFO @ Fri, 10 Dec 2021 18:52:30: start X-correlation... INFO @ Fri, 10 Dec 2021 18:52:30: end of X-cor INFO @ Fri, 10 Dec 2021 18:52:30: #2 finished! INFO @ Fri, 10 Dec 2021 18:52:30: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 18:52:30: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 18:52:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.20_model.r WARNING @ Fri, 10 Dec 2021 18:52:30: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:52:30: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 18:52:30: #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 18:52:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:52:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:52:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978749/ERX3978749.20_summits.bed INFO @ Fri, 10 Dec 2021 18:52:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1737 records, 4 fields): 3 millis CompletedMACS2peakCalling