Job ID = 14167418 SRX = ERX3978904 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17272079 spots for ERR3975973/ERR3975973.sra Written 17272079 spots for ERR3975973/ERR3975973.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168188 ("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: 00:43:07 17272079 reads; of these: 17272079 (100.00%) were paired; of these: 1859615 (10.77%) aligned concordantly 0 times 12397298 (71.78%) aligned concordantly exactly 1 time 3015166 (17.46%) aligned concordantly >1 times ---- 1859615 pairs aligned concordantly 0 times; of these: 360328 (19.38%) aligned discordantly 1 time ---- 1499287 pairs aligned 0 times concordantly or discordantly; of these: 2998574 mates make up the pairs; of these: 1539232 (51.33%) aligned 0 times 659780 (22.00%) aligned exactly 1 time 799562 (26.66%) aligned >1 times 95.54% overall alignment rate Time searching: 00:43:07 Overall time: 00:43:07 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] 11499879 / 15717035 = 0.7317 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 13:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.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 13:06:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:06:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:06:18: 1000000 INFO @ Fri, 10 Dec 2021 13:06:23: 2000000 INFO @ Fri, 10 Dec 2021 13:06:28: 3000000 INFO @ Fri, 10 Dec 2021 13:06:33: 4000000 INFO @ Fri, 10 Dec 2021 13:06:38: 5000000 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 13:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.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 13:06:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:06:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:06:44: 6000000 INFO @ Fri, 10 Dec 2021 13:06:48: 1000000 INFO @ Fri, 10 Dec 2021 13:06:49: 7000000 INFO @ Fri, 10 Dec 2021 13:06:53: 2000000 INFO @ Fri, 10 Dec 2021 13:06:54: 8000000 INFO @ Fri, 10 Dec 2021 13:06:59: 3000000 INFO @ Fri, 10 Dec 2021 13:07:00: 9000000 INFO @ Fri, 10 Dec 2021 13:07:04: 4000000 INFO @ Fri, 10 Dec 2021 13:07:05: 10000000 INFO @ Fri, 10 Dec 2021 13:07:05: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:07:05: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:07:05: #1 total tags in treatment: 4140513 INFO @ Fri, 10 Dec 2021 13:07:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:07:05: #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 13:07:05: #1 tags after filtering in treatment: 3830429 INFO @ Fri, 10 Dec 2021 13:07:05: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 13:07:05: #1 finished! INFO @ Fri, 10 Dec 2021 13:07:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:07:05: #2 number of paired peaks: 4787 INFO @ Fri, 10 Dec 2021 13:07:05: start model_add_line... INFO @ Fri, 10 Dec 2021 13:07:05: start X-correlation... INFO @ Fri, 10 Dec 2021 13:07:05: end of X-cor INFO @ Fri, 10 Dec 2021 13:07:05: #2 finished! INFO @ Fri, 10 Dec 2021 13:07:05: #2 predicted fragment length is 191 bps INFO @ Fri, 10 Dec 2021 13:07:05: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 10 Dec 2021 13:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.05_model.r INFO @ Fri, 10 Dec 2021 13:07:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:07:09: 5000000 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 13:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.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 13:07:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:07:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:07:14: 6000000 INFO @ Fri, 10 Dec 2021 13:07:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:07:18: 1000000 INFO @ Fri, 10 Dec 2021 13:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.05_summits.bed INFO @ Fri, 10 Dec 2021 13:07:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8426 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:07:19: 7000000 INFO @ Fri, 10 Dec 2021 13:07:23: 2000000 INFO @ Fri, 10 Dec 2021 13:07:25: 8000000 INFO @ Fri, 10 Dec 2021 13:07:29: 3000000 INFO @ Fri, 10 Dec 2021 13:07:30: 9000000 INFO @ Fri, 10 Dec 2021 13:07:34: 4000000 INFO @ Fri, 10 Dec 2021 13:07:35: 10000000 INFO @ Fri, 10 Dec 2021 13:07:35: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:07:35: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:07:35: #1 total tags in treatment: 4140513 INFO @ Fri, 10 Dec 2021 13:07:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:07:35: #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 13:07:35: #1 tags after filtering in treatment: 3830429 INFO @ Fri, 10 Dec 2021 13:07:35: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 13:07:35: #1 finished! INFO @ Fri, 10 Dec 2021 13:07:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:07:36: #2 number of paired peaks: 4787 INFO @ Fri, 10 Dec 2021 13:07:36: start model_add_line... INFO @ Fri, 10 Dec 2021 13:07:36: start X-correlation... INFO @ Fri, 10 Dec 2021 13:07:36: end of X-cor INFO @ Fri, 10 Dec 2021 13:07:36: #2 finished! INFO @ Fri, 10 Dec 2021 13:07:36: #2 predicted fragment length is 191 bps INFO @ Fri, 10 Dec 2021 13:07:36: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 10 Dec 2021 13:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.10_model.r INFO @ Fri, 10 Dec 2021 13:07:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:07:39: 5000000 INFO @ Fri, 10 Dec 2021 13:07:44: 6000000 INFO @ Fri, 10 Dec 2021 13:07:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:07:49: 7000000 INFO @ Fri, 10 Dec 2021 13:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.10_summits.bed INFO @ Fri, 10 Dec 2021 13:07:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5553 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:07:54: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:07:59: 9000000 INFO @ Fri, 10 Dec 2021 13:08:04: 10000000 INFO @ Fri, 10 Dec 2021 13:08:04: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 13:08:04: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 13:08:04: #1 total tags in treatment: 4140513 INFO @ Fri, 10 Dec 2021 13:08:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:08:04: #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 13:08:04: #1 tags after filtering in treatment: 3830429 INFO @ Fri, 10 Dec 2021 13:08:04: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 13:08:04: #1 finished! INFO @ Fri, 10 Dec 2021 13:08:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:08:04: #2 number of paired peaks: 4787 INFO @ Fri, 10 Dec 2021 13:08:04: start model_add_line... INFO @ Fri, 10 Dec 2021 13:08:04: start X-correlation... INFO @ Fri, 10 Dec 2021 13:08:04: end of X-cor INFO @ Fri, 10 Dec 2021 13:08:04: #2 finished! INFO @ Fri, 10 Dec 2021 13:08:04: #2 predicted fragment length is 191 bps INFO @ Fri, 10 Dec 2021 13:08:04: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 10 Dec 2021 13:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.20_model.r INFO @ Fri, 10 Dec 2021 13:08:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:08:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978904/ERX3978904.20_summits.bed INFO @ Fri, 10 Dec 2021 13:08:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3079 records, 4 fields): 4 millis CompletedMACS2peakCalling