Job ID = 14168695 SRX = ERX3978761 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11604325 spots for ERR3975776/ERR3975776.sra Written 11604325 spots for ERR3975776/ERR3975776.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169800 ("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: 00:21:23 11604325 reads; of these: 11604325 (100.00%) were paired; of these: 5067335 (43.67%) aligned concordantly 0 times 3001772 (25.87%) aligned concordantly exactly 1 time 3535218 (30.46%) aligned concordantly >1 times ---- 5067335 pairs aligned concordantly 0 times; of these: 796653 (15.72%) aligned discordantly 1 time ---- 4270682 pairs aligned 0 times concordantly or discordantly; of these: 8541364 mates make up the pairs; of these: 5716699 (66.93%) aligned 0 times 199630 (2.34%) aligned exactly 1 time 2625035 (30.73%) aligned >1 times 75.37% overall alignment rate Time searching: 00:21:23 Overall time: 00:21:23 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] 2547944 / 7262939 = 0.3508 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 19:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.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 19:51:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:51:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:51:26: 1000000 INFO @ Fri, 10 Dec 2021 19:51:32: 2000000 INFO @ Fri, 10 Dec 2021 19:51:39: 3000000 INFO @ Fri, 10 Dec 2021 19:51:45: 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 19:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.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 19:51:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:51:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:51:52: 5000000 INFO @ Fri, 10 Dec 2021 19:51:57: 1000000 INFO @ Fri, 10 Dec 2021 19:51:59: 6000000 INFO @ Fri, 10 Dec 2021 19:52:04: 2000000 INFO @ Fri, 10 Dec 2021 19:52:06: 7000000 INFO @ Fri, 10 Dec 2021 19:52:11: 3000000 INFO @ Fri, 10 Dec 2021 19:52:13: 8000000 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 19:52:19: 4000000 INFO @ Fri, 10 Dec 2021 19:52:19: 9000000 INFO @ Fri, 10 Dec 2021 19:52:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.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 19:52:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:52:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:52:26: 5000000 INFO @ Fri, 10 Dec 2021 19:52:27: 10000000 INFO @ Fri, 10 Dec 2021 19:52:29: 1000000 INFO @ Fri, 10 Dec 2021 19:52:34: 6000000 INFO @ Fri, 10 Dec 2021 19:52:34: 11000000 INFO @ Fri, 10 Dec 2021 19:52:38: 2000000 INFO @ Fri, 10 Dec 2021 19:52:42: 7000000 INFO @ Fri, 10 Dec 2021 19:52:42: 12000000 INFO @ Fri, 10 Dec 2021 19:52:45: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:52:45: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:52:45: #1 total tags in treatment: 4058268 INFO @ Fri, 10 Dec 2021 19:52:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:52:45: #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 19:52:45: #1 tags after filtering in treatment: 3001281 INFO @ Fri, 10 Dec 2021 19:52:45: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:52:45: #1 finished! INFO @ Fri, 10 Dec 2021 19:52:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:52:46: #2 number of paired peaks: 4552 INFO @ Fri, 10 Dec 2021 19:52:46: start model_add_line... INFO @ Fri, 10 Dec 2021 19:52:46: start X-correlation... INFO @ Fri, 10 Dec 2021 19:52:46: end of X-cor INFO @ Fri, 10 Dec 2021 19:52:46: #2 finished! INFO @ Fri, 10 Dec 2021 19:52:46: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 19:52:46: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 19:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.05_model.r WARNING @ Fri, 10 Dec 2021 19:52:46: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:52:46: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Fri, 10 Dec 2021 19:52:46: #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 19:52:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:52:48: 3000000 INFO @ Fri, 10 Dec 2021 19:52:49: 8000000 INFO @ Fri, 10 Dec 2021 19:52:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:52:56: 9000000 INFO @ Fri, 10 Dec 2021 19:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.05_summits.bed INFO @ Fri, 10 Dec 2021 19:52:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9426 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:52:57: 4000000 INFO @ Fri, 10 Dec 2021 19:53:04: 10000000 INFO @ Fri, 10 Dec 2021 19:53:06: 5000000 INFO @ Fri, 10 Dec 2021 19:53:11: 11000000 INFO @ Fri, 10 Dec 2021 19:53:15: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:53:19: 12000000 INFO @ Fri, 10 Dec 2021 19:53:22: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:53:22: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:53:22: #1 total tags in treatment: 4058268 INFO @ Fri, 10 Dec 2021 19:53:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:53:22: #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 19:53:22: #1 tags after filtering in treatment: 3001281 INFO @ Fri, 10 Dec 2021 19:53:22: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:53:22: #1 finished! INFO @ Fri, 10 Dec 2021 19:53:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:53:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:53:23: #2 number of paired peaks: 4552 INFO @ Fri, 10 Dec 2021 19:53:23: start model_add_line... INFO @ Fri, 10 Dec 2021 19:53:23: start X-correlation... INFO @ Fri, 10 Dec 2021 19:53:23: end of X-cor INFO @ Fri, 10 Dec 2021 19:53:23: #2 finished! INFO @ Fri, 10 Dec 2021 19:53:23: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 19:53:23: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 19:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.10_model.r WARNING @ Fri, 10 Dec 2021 19:53:23: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:53:23: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Fri, 10 Dec 2021 19:53:23: #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 19:53:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:53:24: 7000000 INFO @ Fri, 10 Dec 2021 19:53:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:53:33: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.10_summits.bed INFO @ Fri, 10 Dec 2021 19:53:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4903 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:53:41: 9000000 INFO @ Fri, 10 Dec 2021 19:53:49: 10000000 INFO @ Fri, 10 Dec 2021 19:53:57: 11000000 INFO @ Fri, 10 Dec 2021 19:54:06: 12000000 INFO @ Fri, 10 Dec 2021 19:54:09: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:54:09: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:54:09: #1 total tags in treatment: 4058268 INFO @ Fri, 10 Dec 2021 19:54:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:54:09: #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 19:54:09: #1 tags after filtering in treatment: 3001281 INFO @ Fri, 10 Dec 2021 19:54:09: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:54:09: #1 finished! INFO @ Fri, 10 Dec 2021 19:54:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:54:10: #2 number of paired peaks: 4552 INFO @ Fri, 10 Dec 2021 19:54:10: start model_add_line... INFO @ Fri, 10 Dec 2021 19:54:10: start X-correlation... INFO @ Fri, 10 Dec 2021 19:54:10: end of X-cor INFO @ Fri, 10 Dec 2021 19:54:10: #2 finished! INFO @ Fri, 10 Dec 2021 19:54:10: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 19:54:10: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 19:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.20_model.r WARNING @ Fri, 10 Dec 2021 19:54:10: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:54:10: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Fri, 10 Dec 2021 19:54:10: #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 19:54:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:54:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:54:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978761/ERX3978761.20_summits.bed INFO @ Fri, 10 Dec 2021 19:54:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1515 records, 4 fields): 3 millis CompletedMACS2peakCalling