Job ID = 14168923 SRX = SRX9217374 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33233645 spots for SRR12744931/SRR12744931.sra Written 33233645 spots for SRR12744931/SRR12744931.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169934 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:49 33233645 reads; of these: 33233645 (100.00%) were paired; of these: 31438088 (94.60%) aligned concordantly 0 times 1304365 (3.92%) aligned concordantly exactly 1 time 491192 (1.48%) aligned concordantly >1 times ---- 31438088 pairs aligned concordantly 0 times; of these: 107746 (0.34%) aligned discordantly 1 time ---- 31330342 pairs aligned 0 times concordantly or discordantly; of these: 62660684 mates make up the pairs; of these: 62591590 (99.89%) aligned 0 times 33194 (0.05%) aligned exactly 1 time 35900 (0.06%) aligned >1 times 5.83% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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_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] 239829 / 1585351 = 0.1513 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 21:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.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 21:53:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:53:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:53:06: 1000000 INFO @ Fri, 10 Dec 2021 21:53:11: 2000000 INFO @ Fri, 10 Dec 2021 21:53:16: 3000000 INFO @ Fri, 10 Dec 2021 21:53:18: #1 tag size is determined as 47 bps INFO @ Fri, 10 Dec 2021 21:53:18: #1 tag size = 47 INFO @ Fri, 10 Dec 2021 21:53:18: #1 total tags in treatment: 1563521 INFO @ Fri, 10 Dec 2021 21:53:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:53:18: #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 21:53:18: #1 tags after filtering in treatment: 1287159 INFO @ Fri, 10 Dec 2021 21:53:18: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Dec 2021 21:53:18: #1 finished! INFO @ Fri, 10 Dec 2021 21:53:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:53:19: #2 number of paired peaks: 3554 INFO @ Fri, 10 Dec 2021 21:53:19: start model_add_line... INFO @ Fri, 10 Dec 2021 21:53:19: start X-correlation... INFO @ Fri, 10 Dec 2021 21:53:19: end of X-cor INFO @ Fri, 10 Dec 2021 21:53:19: #2 finished! INFO @ Fri, 10 Dec 2021 21:53:19: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Dec 2021 21:53:19: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Dec 2021 21:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.05_model.r WARNING @ Fri, 10 Dec 2021 21:53:19: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:53:19: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Dec 2021 21:53:19: #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 21:53:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:53:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.05_summits.bed INFO @ Fri, 10 Dec 2021 21:53:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2183 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 21:53:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.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 21:53:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:53:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:53:36: 1000000 INFO @ Fri, 10 Dec 2021 21:53:42: 2000000 INFO @ Fri, 10 Dec 2021 21:53:47: 3000000 INFO @ Fri, 10 Dec 2021 21:53:49: #1 tag size is determined as 47 bps INFO @ Fri, 10 Dec 2021 21:53:49: #1 tag size = 47 INFO @ Fri, 10 Dec 2021 21:53:49: #1 total tags in treatment: 1563521 INFO @ Fri, 10 Dec 2021 21:53:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:53:49: #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 21:53:49: #1 tags after filtering in treatment: 1287159 INFO @ Fri, 10 Dec 2021 21:53:49: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Dec 2021 21:53:49: #1 finished! INFO @ Fri, 10 Dec 2021 21:53:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:53:49: #2 number of paired peaks: 3554 INFO @ Fri, 10 Dec 2021 21:53:49: start model_add_line... INFO @ Fri, 10 Dec 2021 21:53:49: start X-correlation... INFO @ Fri, 10 Dec 2021 21:53:49: end of X-cor INFO @ Fri, 10 Dec 2021 21:53:49: #2 finished! INFO @ Fri, 10 Dec 2021 21:53:49: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Dec 2021 21:53:49: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Dec 2021 21:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.10_model.r WARNING @ Fri, 10 Dec 2021 21:53:49: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:53:49: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Dec 2021 21:53:49: #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 21:53:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:53:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.10_summits.bed INFO @ Fri, 10 Dec 2021 21:53:53: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 21:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.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 21:54:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:54:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:54:06: 1000000 INFO @ Fri, 10 Dec 2021 21:54:12: 2000000 INFO @ Fri, 10 Dec 2021 21:54:17: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:54:19: #1 tag size is determined as 47 bps INFO @ Fri, 10 Dec 2021 21:54:19: #1 tag size = 47 INFO @ Fri, 10 Dec 2021 21:54:19: #1 total tags in treatment: 1563521 INFO @ Fri, 10 Dec 2021 21:54:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:54:19: #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 21:54:19: #1 tags after filtering in treatment: 1287159 INFO @ Fri, 10 Dec 2021 21:54:19: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 10 Dec 2021 21:54:19: #1 finished! INFO @ Fri, 10 Dec 2021 21:54:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:54:19: #2 number of paired peaks: 3554 INFO @ Fri, 10 Dec 2021 21:54:19: start model_add_line... INFO @ Fri, 10 Dec 2021 21:54:19: start X-correlation... INFO @ Fri, 10 Dec 2021 21:54:19: end of X-cor INFO @ Fri, 10 Dec 2021 21:54:19: #2 finished! INFO @ Fri, 10 Dec 2021 21:54:19: #2 predicted fragment length is 77 bps INFO @ Fri, 10 Dec 2021 21:54:19: #2 alternative fragment length(s) may be 77 bps INFO @ Fri, 10 Dec 2021 21:54:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.20_model.r WARNING @ Fri, 10 Dec 2021 21:54:19: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:54:19: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Fri, 10 Dec 2021 21:54:19: #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 21:54:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:54:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:54:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:54:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:54:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:54:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217374/SRX9217374.20_summits.bed INFO @ Fri, 10 Dec 2021 21:54:24: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。