Job ID = 14168521 SRX = ERX3978754 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14061839 spots for ERR3975767/ERR3975767.sra Written 14061839 spots for ERR3975767/ERR3975767.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169683 ("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: 00:23:38 14061839 reads; of these: 14061839 (100.00%) were paired; of these: 6696628 (47.62%) aligned concordantly 0 times 4510511 (32.08%) aligned concordantly exactly 1 time 2854700 (20.30%) aligned concordantly >1 times ---- 6696628 pairs aligned concordantly 0 times; of these: 1297654 (19.38%) aligned discordantly 1 time ---- 5398974 pairs aligned 0 times concordantly or discordantly; of these: 10797948 mates make up the pairs; of these: 8059078 (74.64%) aligned 0 times 288137 (2.67%) aligned exactly 1 time 2450733 (22.70%) aligned >1 times 71.34% overall alignment rate Time searching: 00:23:38 Overall time: 00:23:38 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] 2104953 / 8578572 = 0.2454 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 19:22:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.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 19:22:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:22:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:22:38: 1000000 INFO @ Fri, 10 Dec 2021 19:22:45: 2000000 INFO @ Fri, 10 Dec 2021 19:22:52: 3000000 INFO @ Fri, 10 Dec 2021 19:22:59: 4000000 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 19:23:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.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 19:23:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:23:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:23:07: 5000000 INFO @ Fri, 10 Dec 2021 19:23:10: 1000000 INFO @ Fri, 10 Dec 2021 19:23:15: 6000000 INFO @ Fri, 10 Dec 2021 19:23:20: 2000000 INFO @ Fri, 10 Dec 2021 19:23:23: 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 19:23:30: 3000000 INFO @ Fri, 10 Dec 2021 19:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.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 19:23:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:23:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:23:31: 8000000 INFO @ Fri, 10 Dec 2021 19:23:39: 4000000 INFO @ Fri, 10 Dec 2021 19:23:39: 1000000 INFO @ Fri, 10 Dec 2021 19:23:40: 9000000 INFO @ Fri, 10 Dec 2021 19:23:48: 2000000 INFO @ Fri, 10 Dec 2021 19:23:48: 10000000 INFO @ Fri, 10 Dec 2021 19:23:49: 5000000 INFO @ Fri, 10 Dec 2021 19:23:56: 3000000 INFO @ Fri, 10 Dec 2021 19:23:56: 11000000 INFO @ Fri, 10 Dec 2021 19:23:59: 6000000 INFO @ Fri, 10 Dec 2021 19:24:05: 12000000 INFO @ Fri, 10 Dec 2021 19:24:05: 4000000 INFO @ Fri, 10 Dec 2021 19:24:08: 7000000 INFO @ Fri, 10 Dec 2021 19:24:13: 13000000 INFO @ Fri, 10 Dec 2021 19:24:13: 5000000 INFO @ Fri, 10 Dec 2021 19:24:18: 8000000 INFO @ Fri, 10 Dec 2021 19:24:21: 14000000 INFO @ Fri, 10 Dec 2021 19:24:22: 6000000 INFO @ Fri, 10 Dec 2021 19:24:28: 9000000 INFO @ Fri, 10 Dec 2021 19:24:30: 15000000 INFO @ Fri, 10 Dec 2021 19:24:31: 7000000 INFO @ Fri, 10 Dec 2021 19:24:37: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:24:37: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:24:37: #1 total tags in treatment: 5382657 INFO @ Fri, 10 Dec 2021 19:24:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:24:37: #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 19:24:37: 10000000 INFO @ Fri, 10 Dec 2021 19:24:37: #1 tags after filtering in treatment: 4151493 INFO @ Fri, 10 Dec 2021 19:24:37: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Dec 2021 19:24:37: #1 finished! INFO @ Fri, 10 Dec 2021 19:24:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:24:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:24:38: #2 number of paired peaks: 4306 INFO @ Fri, 10 Dec 2021 19:24:38: start model_add_line... INFO @ Fri, 10 Dec 2021 19:24:38: start X-correlation... INFO @ Fri, 10 Dec 2021 19:24:38: end of X-cor INFO @ Fri, 10 Dec 2021 19:24:38: #2 finished! INFO @ Fri, 10 Dec 2021 19:24:38: #2 predicted fragment length is 178 bps INFO @ Fri, 10 Dec 2021 19:24:38: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 10 Dec 2021 19:24:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.05_model.r WARNING @ Fri, 10 Dec 2021 19:24:38: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:24:38: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Fri, 10 Dec 2021 19:24:38: #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 19:24:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:24:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:24:39: 8000000 INFO @ Fri, 10 Dec 2021 19:24:46: 11000000 INFO @ Fri, 10 Dec 2021 19:24:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:24:47: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:24:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.05_summits.bed INFO @ Fri, 10 Dec 2021 19:24:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10640 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:24:55: 12000000 INFO @ Fri, 10 Dec 2021 19:24:56: 10000000 INFO @ Fri, 10 Dec 2021 19:25:03: 11000000 INFO @ Fri, 10 Dec 2021 19:25:05: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:25:11: 12000000 INFO @ Fri, 10 Dec 2021 19:25:14: 14000000 INFO @ Fri, 10 Dec 2021 19:25:19: 13000000 INFO @ Fri, 10 Dec 2021 19:25:24: 15000000 INFO @ Fri, 10 Dec 2021 19:25:27: 14000000 INFO @ Fri, 10 Dec 2021 19:25:32: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:25:32: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:25:32: #1 total tags in treatment: 5382657 INFO @ Fri, 10 Dec 2021 19:25:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:25:32: #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 19:25:32: #1 tags after filtering in treatment: 4151493 INFO @ Fri, 10 Dec 2021 19:25:32: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Dec 2021 19:25:32: #1 finished! INFO @ Fri, 10 Dec 2021 19:25:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:25:32: #2 number of paired peaks: 4306 INFO @ Fri, 10 Dec 2021 19:25:32: start model_add_line... INFO @ Fri, 10 Dec 2021 19:25:32: start X-correlation... INFO @ Fri, 10 Dec 2021 19:25:32: end of X-cor INFO @ Fri, 10 Dec 2021 19:25:32: #2 finished! INFO @ Fri, 10 Dec 2021 19:25:32: #2 predicted fragment length is 178 bps INFO @ Fri, 10 Dec 2021 19:25:32: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 10 Dec 2021 19:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.10_model.r WARNING @ Fri, 10 Dec 2021 19:25:32: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:25:32: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Fri, 10 Dec 2021 19:25:32: #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 19:25:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:25:35: 15000000 INFO @ Fri, 10 Dec 2021 19:25:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:25:42: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:25:42: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:25:42: #1 total tags in treatment: 5382657 INFO @ Fri, 10 Dec 2021 19:25:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:25:42: #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 19:25:42: #1 tags after filtering in treatment: 4151493 INFO @ Fri, 10 Dec 2021 19:25:42: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Dec 2021 19:25:42: #1 finished! INFO @ Fri, 10 Dec 2021 19:25:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:25:42: #2 number of paired peaks: 4306 INFO @ Fri, 10 Dec 2021 19:25:42: start model_add_line... INFO @ Fri, 10 Dec 2021 19:25:42: start X-correlation... INFO @ Fri, 10 Dec 2021 19:25:42: end of X-cor INFO @ Fri, 10 Dec 2021 19:25:42: #2 finished! INFO @ Fri, 10 Dec 2021 19:25:42: #2 predicted fragment length is 178 bps INFO @ Fri, 10 Dec 2021 19:25:42: #2 alternative fragment length(s) may be 178 bps INFO @ Fri, 10 Dec 2021 19:25:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.20_model.r WARNING @ Fri, 10 Dec 2021 19:25:42: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:25:42: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Fri, 10 Dec 2021 19:25:42: #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 19:25:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:25:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.10_summits.bed INFO @ Fri, 10 Dec 2021 19:25:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5615 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:25:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978754/ERX3978754.20_summits.bed INFO @ Fri, 10 Dec 2021 19:25:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1881 records, 4 fields): 4 millis CompletedMACS2peakCalling