Job ID = 14168271 SRX = ERX3978846 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16506190 spots for ERR3975915/ERR3975915.sra Written 16506190 spots for ERR3975915/ERR3975915.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169428 ("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: 00:44:09 16506190 reads; of these: 16506190 (100.00%) were paired; of these: 1990775 (12.06%) aligned concordantly 0 times 12197411 (73.90%) aligned concordantly exactly 1 time 2318004 (14.04%) aligned concordantly >1 times ---- 1990775 pairs aligned concordantly 0 times; of these: 499748 (25.10%) aligned discordantly 1 time ---- 1491027 pairs aligned 0 times concordantly or discordantly; of these: 2982054 mates make up the pairs; of these: 1354958 (45.44%) aligned 0 times 914106 (30.65%) aligned exactly 1 time 712990 (23.91%) aligned >1 times 95.90% overall alignment rate Time searching: 00:44:09 Overall time: 00:44:09 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 16 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] 11146408 / 14972231 = 0.7445 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 17:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.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 17:36:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:36:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:36:27: 1000000 INFO @ Fri, 10 Dec 2021 17:36:33: 2000000 INFO @ Fri, 10 Dec 2021 17:36:39: 3000000 INFO @ Fri, 10 Dec 2021 17:36:45: 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 17:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.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 17:36:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:36:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:36:51: 5000000 INFO @ Fri, 10 Dec 2021 17:36:58: 6000000 INFO @ Fri, 10 Dec 2021 17:36:58: 1000000 INFO @ Fri, 10 Dec 2021 17:37:05: 7000000 INFO @ Fri, 10 Dec 2021 17:37:05: 2000000 INFO @ Fri, 10 Dec 2021 17:37:12: 8000000 INFO @ Fri, 10 Dec 2021 17:37:13: 3000000 INFO @ Fri, 10 Dec 2021 17:37:18: 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 17:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.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 17:37:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:37:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:37:21: 4000000 INFO @ Fri, 10 Dec 2021 17:37:21: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:37:21: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:37:21: #1 total tags in treatment: 3659820 INFO @ Fri, 10 Dec 2021 17:37:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:37:21: #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 17:37:21: #1 tags after filtering in treatment: 3365107 INFO @ Fri, 10 Dec 2021 17:37:21: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:37:21: #1 finished! INFO @ Fri, 10 Dec 2021 17:37:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:37:21: #2 number of paired peaks: 2340 INFO @ Fri, 10 Dec 2021 17:37:21: start model_add_line... INFO @ Fri, 10 Dec 2021 17:37:21: start X-correlation... INFO @ Fri, 10 Dec 2021 17:37:21: end of X-cor INFO @ Fri, 10 Dec 2021 17:37:21: #2 finished! INFO @ Fri, 10 Dec 2021 17:37:21: #2 predicted fragment length is 164 bps INFO @ Fri, 10 Dec 2021 17:37:21: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 10 Dec 2021 17:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.05_model.r INFO @ Fri, 10 Dec 2021 17:37:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:37:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:37:27: 1000000 INFO @ Fri, 10 Dec 2021 17:37:28: 5000000 INFO @ Fri, 10 Dec 2021 17:37:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:37:33: 2000000 INFO @ Fri, 10 Dec 2021 17:37:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:37:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:37:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.05_summits.bed INFO @ Fri, 10 Dec 2021 17:37:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4406 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:37:36: 6000000 INFO @ Fri, 10 Dec 2021 17:37:39: 3000000 INFO @ Fri, 10 Dec 2021 17:37:44: 7000000 INFO @ Fri, 10 Dec 2021 17:37:45: 4000000 INFO @ Fri, 10 Dec 2021 17:37:52: 8000000 INFO @ Fri, 10 Dec 2021 17:37:52: 5000000 INFO @ Fri, 10 Dec 2021 17:37:58: 6000000 INFO @ Fri, 10 Dec 2021 17:37:59: 9000000 INFO @ Fri, 10 Dec 2021 17:38:02: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:38:02: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:38:02: #1 total tags in treatment: 3659820 INFO @ Fri, 10 Dec 2021 17:38:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:38:02: #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 17:38:02: #1 tags after filtering in treatment: 3365107 INFO @ Fri, 10 Dec 2021 17:38:02: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:38:02: #1 finished! INFO @ Fri, 10 Dec 2021 17:38:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:38:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:38:02: #2 number of paired peaks: 2340 INFO @ Fri, 10 Dec 2021 17:38:02: start model_add_line... INFO @ Fri, 10 Dec 2021 17:38:02: start X-correlation... INFO @ Fri, 10 Dec 2021 17:38:02: end of X-cor INFO @ Fri, 10 Dec 2021 17:38:02: #2 finished! INFO @ Fri, 10 Dec 2021 17:38:02: #2 predicted fragment length is 164 bps INFO @ Fri, 10 Dec 2021 17:38:02: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 10 Dec 2021 17:38:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.10_model.r INFO @ Fri, 10 Dec 2021 17:38:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:38:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:38:04: 7000000 INFO @ Fri, 10 Dec 2021 17:38:10: 8000000 INFO @ Fri, 10 Dec 2021 17:38:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.10_summits.bed INFO @ Fri, 10 Dec 2021 17:38:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1945 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:38:15: 9000000 INFO @ Fri, 10 Dec 2021 17:38:17: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:38:17: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:38:17: #1 total tags in treatment: 3659820 INFO @ Fri, 10 Dec 2021 17:38:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:38:17: #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 17:38:17: #1 tags after filtering in treatment: 3365107 INFO @ Fri, 10 Dec 2021 17:38:17: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:38:17: #1 finished! INFO @ Fri, 10 Dec 2021 17:38:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:38:17: #2 number of paired peaks: 2340 INFO @ Fri, 10 Dec 2021 17:38:17: start model_add_line... INFO @ Fri, 10 Dec 2021 17:38:17: start X-correlation... INFO @ Fri, 10 Dec 2021 17:38:17: end of X-cor INFO @ Fri, 10 Dec 2021 17:38:17: #2 finished! INFO @ Fri, 10 Dec 2021 17:38:17: #2 predicted fragment length is 164 bps INFO @ Fri, 10 Dec 2021 17:38:17: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 10 Dec 2021 17:38:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.20_model.r INFO @ Fri, 10 Dec 2021 17:38:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:38:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:38:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978846/ERX3978846.20_summits.bed INFO @ Fri, 10 Dec 2021 17:38:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 3 millis CompletedMACS2peakCalling