Job ID = 14171447 SRX = SRX9555293 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9198515 spots for SRR13110743/SRR13110743.sra Written 9198515 spots for SRR13110743/SRR13110743.sra Read 9114301 spots for SRR13110744/SRR13110744.sra Written 9114301 spots for SRR13110744/SRR13110744.sra Read 9217625 spots for SRR13110745/SRR13110745.sra Written 9217625 spots for SRR13110745/SRR13110745.sra Read 9150422 spots for SRR13110746/SRR13110746.sra Written 9150422 spots for SRR13110746/SRR13110746.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171954 ("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: 00:06:15 36680863 reads; of these: 36680863 (100.00%) were paired; of these: 34956975 (95.30%) aligned concordantly 0 times 1302228 (3.55%) aligned concordantly exactly 1 time 421660 (1.15%) aligned concordantly >1 times ---- 34956975 pairs aligned concordantly 0 times; of these: 4673 (0.01%) aligned discordantly 1 time ---- 34952302 pairs aligned 0 times concordantly or discordantly; of these: 69904604 mates make up the pairs; of these: 69663335 (99.65%) aligned 0 times 95073 (0.14%) aligned exactly 1 time 146196 (0.21%) aligned >1 times 5.04% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 79368 / 1727607 = 0.0459 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 11:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.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 11:51:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:51:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:51:43: 1000000 INFO @ Sat, 11 Dec 2021 11:51:47: 2000000 INFO @ Sat, 11 Dec 2021 11:51:51: 3000000 INFO @ Sat, 11 Dec 2021 11:51:53: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:51:53: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:51:53: #1 total tags in treatment: 1644593 INFO @ Sat, 11 Dec 2021 11:51:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:51:53: #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 11:51:53: #1 tags after filtering in treatment: 1443280 INFO @ Sat, 11 Dec 2021 11:51:53: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 11:51:53: #1 finished! INFO @ Sat, 11 Dec 2021 11:51:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:51:54: #2 number of paired peaks: 7232 INFO @ Sat, 11 Dec 2021 11:51:54: start model_add_line... INFO @ Sat, 11 Dec 2021 11:51:54: start X-correlation... INFO @ Sat, 11 Dec 2021 11:51:54: end of X-cor INFO @ Sat, 11 Dec 2021 11:51:54: #2 finished! INFO @ Sat, 11 Dec 2021 11:51:54: #2 predicted fragment length is 161 bps INFO @ Sat, 11 Dec 2021 11:51:54: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 11 Dec 2021 11:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.05_model.r INFO @ Sat, 11 Dec 2021 11:51:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:51:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:51:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:51:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:51:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.05_summits.bed INFO @ Sat, 11 Dec 2021 11:51:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3618 records, 4 fields): 6 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 11:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.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 11:52:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:13: 1000000 INFO @ Sat, 11 Dec 2021 11:52:17: 2000000 INFO @ Sat, 11 Dec 2021 11:52:21: 3000000 INFO @ Sat, 11 Dec 2021 11:52:23: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:52:23: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:52:23: #1 total tags in treatment: 1644593 INFO @ Sat, 11 Dec 2021 11:52:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:23: #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 11:52:23: #1 tags after filtering in treatment: 1443280 INFO @ Sat, 11 Dec 2021 11:52:23: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 11:52:23: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:23: #2 number of paired peaks: 7232 INFO @ Sat, 11 Dec 2021 11:52:23: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:23: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:23: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:23: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:23: #2 predicted fragment length is 161 bps INFO @ Sat, 11 Dec 2021 11:52:23: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 11 Dec 2021 11:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.10_model.r INFO @ Sat, 11 Dec 2021 11:52:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.10_summits.bed INFO @ Sat, 11 Dec 2021 11:52:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1356 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 11:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.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 11:52:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:45: 1000000 INFO @ Sat, 11 Dec 2021 11:52:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:52:56: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:52:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:52:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:52:58: #1 total tags in treatment: 1644593 INFO @ Sat, 11 Dec 2021 11:52:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:58: #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 11:52:58: #1 tags after filtering in treatment: 1443280 INFO @ Sat, 11 Dec 2021 11:52:58: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 11:52:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:59: #2 number of paired peaks: 7232 INFO @ Sat, 11 Dec 2021 11:52:59: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:59: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:59: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:59: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:59: #2 predicted fragment length is 161 bps INFO @ Sat, 11 Dec 2021 11:52:59: #2 alternative fragment length(s) may be 161 bps INFO @ Sat, 11 Dec 2021 11:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.20_model.r INFO @ Sat, 11 Dec 2021 11:52:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555293/SRX9555293.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling