Job ID = 14171121 SRX = SRX9555310 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7976214 spots for SRR13110427/SRR13110427.sra Written 7976214 spots for SRR13110427/SRR13110427.sra Read 7910152 spots for SRR13110428/SRR13110428.sra Written 7910152 spots for SRR13110428/SRR13110428.sra Read 8130558 spots for SRR13110429/SRR13110429.sra Written 8130558 spots for SRR13110429/SRR13110429.sra Read 8005553 spots for SRR13110430/SRR13110430.sra Written 8005553 spots for SRR13110430/SRR13110430.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171589 ("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: 00:05:22 32022477 reads; of these: 32022477 (100.00%) were paired; of these: 30642394 (95.69%) aligned concordantly 0 times 1117142 (3.49%) aligned concordantly exactly 1 time 262941 (0.82%) aligned concordantly >1 times ---- 30642394 pairs aligned concordantly 0 times; of these: 15220 (0.05%) aligned discordantly 1 time ---- 30627174 pairs aligned 0 times concordantly or discordantly; of these: 61254348 mates make up the pairs; of these: 61000033 (99.58%) aligned 0 times 98724 (0.16%) aligned exactly 1 time 155591 (0.25%) aligned >1 times 4.75% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 37892 / 1394684 = 0.0272 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 @ Sat, 11 Dec 2021 09:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.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 @ Sat, 11 Dec 2021 09:48:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:48:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:48:56: 1000000 INFO @ Sat, 11 Dec 2021 09:49:00: 2000000 INFO @ Sat, 11 Dec 2021 09:49:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:49:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:49:04: #1 total tags in treatment: 1342387 INFO @ Sat, 11 Dec 2021 09:49:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:49:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:49:04: #1 tags after filtering in treatment: 1260783 INFO @ Sat, 11 Dec 2021 09:49:04: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:49:04: #1 finished! INFO @ Sat, 11 Dec 2021 09:49:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:49:05: #2 number of paired peaks: 5633 INFO @ Sat, 11 Dec 2021 09:49:05: start model_add_line... INFO @ Sat, 11 Dec 2021 09:49:05: start X-correlation... INFO @ Sat, 11 Dec 2021 09:49:05: end of X-cor INFO @ Sat, 11 Dec 2021 09:49:05: #2 finished! INFO @ Sat, 11 Dec 2021 09:49:05: #2 predicted fragment length is 222 bps INFO @ Sat, 11 Dec 2021 09:49:05: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 11 Dec 2021 09:49:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.05_model.r INFO @ Sat, 11 Dec 2021 09:49:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:49:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:49:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.05_summits.bed INFO @ Sat, 11 Dec 2021 09:49:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (979 records, 4 fields): 3 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 @ Sat, 11 Dec 2021 09:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.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 @ Sat, 11 Dec 2021 09:49:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:49:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:49:26: 1000000 INFO @ Sat, 11 Dec 2021 09:49:30: 2000000 INFO @ Sat, 11 Dec 2021 09:49:34: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:49:34: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:49:34: #1 total tags in treatment: 1342387 INFO @ Sat, 11 Dec 2021 09:49:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:49:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:49:34: #1 tags after filtering in treatment: 1260783 INFO @ Sat, 11 Dec 2021 09:49:34: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:49:34: #1 finished! INFO @ Sat, 11 Dec 2021 09:49:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:49:34: #2 number of paired peaks: 5633 INFO @ Sat, 11 Dec 2021 09:49:34: start model_add_line... INFO @ Sat, 11 Dec 2021 09:49:34: start X-correlation... INFO @ Sat, 11 Dec 2021 09:49:34: end of X-cor INFO @ Sat, 11 Dec 2021 09:49:34: #2 finished! INFO @ Sat, 11 Dec 2021 09:49:34: #2 predicted fragment length is 222 bps INFO @ Sat, 11 Dec 2021 09:49:34: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 11 Dec 2021 09:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.10_model.r INFO @ Sat, 11 Dec 2021 09:49:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:49:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.10_summits.bed INFO @ Sat, 11 Dec 2021 09:49:39: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (335 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 @ Sat, 11 Dec 2021 09:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.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 @ Sat, 11 Dec 2021 09:49:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:49:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:49:55: 1000000 INFO @ Sat, 11 Dec 2021 09:50:00: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:50:04: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 09:50:04: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 09:50:04: #1 total tags in treatment: 1342387 INFO @ Sat, 11 Dec 2021 09:50:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:50:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:50:04: #1 tags after filtering in treatment: 1260783 INFO @ Sat, 11 Dec 2021 09:50:04: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 09:50:04: #1 finished! INFO @ Sat, 11 Dec 2021 09:50:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:50:04: #2 number of paired peaks: 5633 INFO @ Sat, 11 Dec 2021 09:50:04: start model_add_line... INFO @ Sat, 11 Dec 2021 09:50:04: start X-correlation... INFO @ Sat, 11 Dec 2021 09:50:04: end of X-cor INFO @ Sat, 11 Dec 2021 09:50:04: #2 finished! INFO @ Sat, 11 Dec 2021 09:50:04: #2 predicted fragment length is 222 bps INFO @ Sat, 11 Dec 2021 09:50:04: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 11 Dec 2021 09:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.20_model.r INFO @ Sat, 11 Dec 2021 09:50:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:50:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555310/SRX9555310.20_summits.bed INFO @ Sat, 11 Dec 2021 09:50:08: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling