Job ID = 14167376 SRX = ERX3978900 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17435547 spots for ERR3975969/ERR3975969.sra Written 17435547 spots for ERR3975969/ERR3975969.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168292 ("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: 01:21:50 17435547 reads; of these: 17435547 (100.00%) were paired; of these: 6492127 (37.24%) aligned concordantly 0 times 8358566 (47.94%) aligned concordantly exactly 1 time 2584854 (14.83%) aligned concordantly >1 times ---- 6492127 pairs aligned concordantly 0 times; of these: 492838 (7.59%) aligned discordantly 1 time ---- 5999289 pairs aligned 0 times concordantly or discordantly; of these: 11998578 mates make up the pairs; of these: 5718657 (47.66%) aligned 0 times 3640624 (30.34%) aligned exactly 1 time 2639297 (22.00%) aligned >1 times 83.60% overall alignment rate Time searching: 01:21:50 Overall time: 01:21:50 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] 9049329 / 11264534 = 0.8033 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 13:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.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 13:34:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:34:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:34:15: 1000000 INFO @ Fri, 10 Dec 2021 13:34:21: 2000000 INFO @ Fri, 10 Dec 2021 13:34:27: 3000000 INFO @ Fri, 10 Dec 2021 13:34:33: 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 13:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.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 13:34:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:34:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:34:39: 5000000 INFO @ Fri, 10 Dec 2021 13:34:44: 1000000 INFO @ Fri, 10 Dec 2021 13:34:46: 6000000 INFO @ Fri, 10 Dec 2021 13:34:51: 2000000 INFO @ Fri, 10 Dec 2021 13:34:52: 7000000 INFO @ Fri, 10 Dec 2021 13:34:57: 3000000 INFO @ Fri, 10 Dec 2021 13:34:59: 8000000 INFO @ Fri, 10 Dec 2021 13:35:03: 4000000 INFO @ Fri, 10 Dec 2021 13:35:06: 9000000 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 13:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.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 13:35:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:35:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:35:09: 5000000 INFO @ Fri, 10 Dec 2021 13:35:12: 10000000 INFO @ Fri, 10 Dec 2021 13:35:14: 1000000 INFO @ Fri, 10 Dec 2021 13:35:16: 6000000 INFO @ Fri, 10 Dec 2021 13:35:19: 11000000 INFO @ Fri, 10 Dec 2021 13:35:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:35:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:35:19: #1 total tags in treatment: 2201149 INFO @ Fri, 10 Dec 2021 13:35:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:35:19: #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 13:35:19: #1 tags after filtering in treatment: 1898390 INFO @ Fri, 10 Dec 2021 13:35:19: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 13:35:19: #1 finished! INFO @ Fri, 10 Dec 2021 13:35:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:35:19: #2 number of paired peaks: 4007 INFO @ Fri, 10 Dec 2021 13:35:19: start model_add_line... INFO @ Fri, 10 Dec 2021 13:35:19: start X-correlation... INFO @ Fri, 10 Dec 2021 13:35:19: end of X-cor INFO @ Fri, 10 Dec 2021 13:35:19: #2 finished! INFO @ Fri, 10 Dec 2021 13:35:19: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 13:35:19: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 13:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.05_model.r WARNING @ Fri, 10 Dec 2021 13:35:19: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:35:19: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 13:35:19: #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 13:35:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:35:21: 2000000 INFO @ Fri, 10 Dec 2021 13:35:22: 7000000 INFO @ Fri, 10 Dec 2021 13:35:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.05_summits.bed INFO @ Fri, 10 Dec 2021 13:35:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5800 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:35:27: 3000000 INFO @ Fri, 10 Dec 2021 13:35:29: 8000000 INFO @ Fri, 10 Dec 2021 13:35:34: 4000000 INFO @ Fri, 10 Dec 2021 13:35:35: 9000000 INFO @ Fri, 10 Dec 2021 13:35:40: 5000000 INFO @ Fri, 10 Dec 2021 13:35:42: 10000000 INFO @ Fri, 10 Dec 2021 13:35:46: 6000000 INFO @ Fri, 10 Dec 2021 13:35:48: 11000000 INFO @ Fri, 10 Dec 2021 13:35:48: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:35:48: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:35:48: #1 total tags in treatment: 2201149 INFO @ Fri, 10 Dec 2021 13:35:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:35:48: #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 13:35:48: #1 tags after filtering in treatment: 1898390 INFO @ Fri, 10 Dec 2021 13:35:48: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 13:35:48: #1 finished! INFO @ Fri, 10 Dec 2021 13:35:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:35:49: #2 number of paired peaks: 4007 INFO @ Fri, 10 Dec 2021 13:35:49: start model_add_line... INFO @ Fri, 10 Dec 2021 13:35:49: start X-correlation... INFO @ Fri, 10 Dec 2021 13:35:49: end of X-cor INFO @ Fri, 10 Dec 2021 13:35:49: #2 finished! INFO @ Fri, 10 Dec 2021 13:35:49: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 13:35:49: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 13:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.10_model.r WARNING @ Fri, 10 Dec 2021 13:35:49: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:35:49: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 13:35:49: #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 13:35:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:35:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:35:53: 7000000 INFO @ Fri, 10 Dec 2021 13:35:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:35:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:35:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:35:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.10_summits.bed INFO @ Fri, 10 Dec 2021 13:35:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2334 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:35:59: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:36:05: 9000000 INFO @ Fri, 10 Dec 2021 13:36:12: 10000000 INFO @ Fri, 10 Dec 2021 13:36:18: 11000000 INFO @ Fri, 10 Dec 2021 13:36:18: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:36:18: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:36:18: #1 total tags in treatment: 2201149 INFO @ Fri, 10 Dec 2021 13:36:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:36:18: #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 13:36:18: #1 tags after filtering in treatment: 1898390 INFO @ Fri, 10 Dec 2021 13:36:18: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 13:36:18: #1 finished! INFO @ Fri, 10 Dec 2021 13:36:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:36:18: #2 number of paired peaks: 4007 INFO @ Fri, 10 Dec 2021 13:36:18: start model_add_line... INFO @ Fri, 10 Dec 2021 13:36:18: start X-correlation... INFO @ Fri, 10 Dec 2021 13:36:18: end of X-cor INFO @ Fri, 10 Dec 2021 13:36:18: #2 finished! INFO @ Fri, 10 Dec 2021 13:36:18: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 13:36:18: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 13:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.20_model.r WARNING @ Fri, 10 Dec 2021 13:36:18: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:36:18: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 13:36:18: #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 13:36:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:36:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:36:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:36:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:36:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978900/ERX3978900.20_summits.bed INFO @ Fri, 10 Dec 2021 13:36:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 2 millis CompletedMACS2peakCalling