Job ID = 14168668 SRX = ERX3978876 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33343260 spots for ERR3975945/ERR3975945.sra Written 33343260 spots for ERR3975945/ERR3975945.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169893 ("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: 01:49:30 33343260 reads; of these: 33343260 (100.00%) were paired; of these: 4733420 (14.20%) aligned concordantly 0 times 22337955 (66.99%) aligned concordantly exactly 1 time 6271885 (18.81%) aligned concordantly >1 times ---- 4733420 pairs aligned concordantly 0 times; of these: 713587 (15.08%) aligned discordantly 1 time ---- 4019833 pairs aligned 0 times concordantly or discordantly; of these: 8039666 mates make up the pairs; of these: 5133807 (63.86%) aligned 0 times 1422610 (17.69%) aligned exactly 1 time 1483249 (18.45%) aligned >1 times 92.30% overall alignment rate Time searching: 01:49:30 Overall time: 01:49:30 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 28 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] 18538006 / 29195955 = 0.6350 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 21:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.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 21:32:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:32:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:32:35: 1000000 INFO @ Fri, 10 Dec 2021 21:32:44: 2000000 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 21:32:53: 3000000 INFO @ Fri, 10 Dec 2021 21:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.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 21:32:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:32:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:33:02: 4000000 INFO @ Fri, 10 Dec 2021 21:33:08: 1000000 INFO @ Fri, 10 Dec 2021 21:33:11: 5000000 INFO @ Fri, 10 Dec 2021 21:33:20: 6000000 INFO @ Fri, 10 Dec 2021 21:33:20: 2000000 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 21:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.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 21:33:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:33:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:33:29: 7000000 INFO @ Fri, 10 Dec 2021 21:33:33: 3000000 INFO @ Fri, 10 Dec 2021 21:33:37: 1000000 INFO @ Fri, 10 Dec 2021 21:33:38: 8000000 INFO @ Fri, 10 Dec 2021 21:33:45: 4000000 INFO @ Fri, 10 Dec 2021 21:33:47: 9000000 INFO @ Fri, 10 Dec 2021 21:33:48: 2000000 INFO @ Fri, 10 Dec 2021 21:33:56: 10000000 INFO @ Fri, 10 Dec 2021 21:33:58: 5000000 INFO @ Fri, 10 Dec 2021 21:33:59: 3000000 INFO @ Fri, 10 Dec 2021 21:34:05: 11000000 INFO @ Fri, 10 Dec 2021 21:34:10: 4000000 INFO @ Fri, 10 Dec 2021 21:34:11: 6000000 INFO @ Fri, 10 Dec 2021 21:34:14: 12000000 INFO @ Fri, 10 Dec 2021 21:34:21: 5000000 INFO @ Fri, 10 Dec 2021 21:34:23: 13000000 INFO @ Fri, 10 Dec 2021 21:34:23: 7000000 INFO @ Fri, 10 Dec 2021 21:34:32: 14000000 INFO @ Fri, 10 Dec 2021 21:34:32: 6000000 INFO @ Fri, 10 Dec 2021 21:34:36: 8000000 INFO @ Fri, 10 Dec 2021 21:34:41: 15000000 INFO @ Fri, 10 Dec 2021 21:34:43: 7000000 INFO @ Fri, 10 Dec 2021 21:34:48: 9000000 INFO @ Fri, 10 Dec 2021 21:34:50: 16000000 INFO @ Fri, 10 Dec 2021 21:34:54: 8000000 INFO @ Fri, 10 Dec 2021 21:35:00: 17000000 INFO @ Fri, 10 Dec 2021 21:35:00: 10000000 INFO @ Fri, 10 Dec 2021 21:35:05: 9000000 INFO @ Fri, 10 Dec 2021 21:35:09: 18000000 INFO @ Fri, 10 Dec 2021 21:35:13: 11000000 INFO @ Fri, 10 Dec 2021 21:35:16: 10000000 INFO @ Fri, 10 Dec 2021 21:35:18: 19000000 INFO @ Fri, 10 Dec 2021 21:35:25: 12000000 INFO @ Fri, 10 Dec 2021 21:35:27: 11000000 INFO @ Fri, 10 Dec 2021 21:35:27: 20000000 INFO @ Fri, 10 Dec 2021 21:35:36: 21000000 INFO @ Fri, 10 Dec 2021 21:35:37: 13000000 INFO @ Fri, 10 Dec 2021 21:35:38: 12000000 INFO @ Fri, 10 Dec 2021 21:35:46: 22000000 INFO @ Fri, 10 Dec 2021 21:35:49: 13000000 INFO @ Fri, 10 Dec 2021 21:35:49: 14000000 INFO @ Fri, 10 Dec 2021 21:35:55: 23000000 INFO @ Fri, 10 Dec 2021 21:36:00: 14000000 INFO @ Fri, 10 Dec 2021 21:36:02: 15000000 INFO @ Fri, 10 Dec 2021 21:36:04: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:36:09: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:36:09: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:36:09: #1 total tags in treatment: 10537917 INFO @ Fri, 10 Dec 2021 21:36:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:36:09: #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 21:36:09: #1 tags after filtering in treatment: 9782629 INFO @ Fri, 10 Dec 2021 21:36:09: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 21:36:09: #1 finished! INFO @ Fri, 10 Dec 2021 21:36:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:36:10: #2 number of paired peaks: 531 WARNING @ Fri, 10 Dec 2021 21:36:10: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Fri, 10 Dec 2021 21:36:10: start model_add_line... INFO @ Fri, 10 Dec 2021 21:36:10: start X-correlation... INFO @ Fri, 10 Dec 2021 21:36:10: end of X-cor INFO @ Fri, 10 Dec 2021 21:36:10: #2 finished! INFO @ Fri, 10 Dec 2021 21:36:10: #2 predicted fragment length is 168 bps INFO @ Fri, 10 Dec 2021 21:36:10: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 10 Dec 2021 21:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.05_model.r INFO @ Fri, 10 Dec 2021 21:36:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:36:11: 15000000 INFO @ Fri, 10 Dec 2021 21:36:14: 16000000 INFO @ Fri, 10 Dec 2021 21:36:23: 16000000 INFO @ Fri, 10 Dec 2021 21:36:27: 17000000 INFO @ Fri, 10 Dec 2021 21:36:34: 17000000 INFO @ Fri, 10 Dec 2021 21:36:39: 18000000 INFO @ Fri, 10 Dec 2021 21:36:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:36:44: 18000000 INFO @ Fri, 10 Dec 2021 21:36:51: 19000000 INFO @ Fri, 10 Dec 2021 21:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.05_summits.bed INFO @ Fri, 10 Dec 2021 21:36:55: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8254 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:36:55: 19000000 INFO @ Fri, 10 Dec 2021 21:37:04: 20000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:37:06: 20000000 INFO @ Fri, 10 Dec 2021 21:37:16: 21000000 INFO @ Fri, 10 Dec 2021 21:37:18: 21000000 INFO @ Fri, 10 Dec 2021 21:37:28: 22000000 INFO @ Fri, 10 Dec 2021 21:37:29: 22000000 INFO @ Fri, 10 Dec 2021 21:37:39: 23000000 INFO @ Fri, 10 Dec 2021 21:37:40: 23000000 INFO @ Fri, 10 Dec 2021 21:37:50: 24000000 INFO @ Fri, 10 Dec 2021 21:37:52: 24000000 INFO @ Fri, 10 Dec 2021 21:37:55: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:37:55: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:37:55: #1 total tags in treatment: 10537917 INFO @ Fri, 10 Dec 2021 21:37:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:37:55: #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 21:37:55: #1 tags after filtering in treatment: 9782629 INFO @ Fri, 10 Dec 2021 21:37:55: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 21:37:55: #1 finished! INFO @ Fri, 10 Dec 2021 21:37:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:37:56: #2 number of paired peaks: 531 WARNING @ Fri, 10 Dec 2021 21:37:56: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Fri, 10 Dec 2021 21:37:56: start model_add_line... INFO @ Fri, 10 Dec 2021 21:37:56: start X-correlation... INFO @ Fri, 10 Dec 2021 21:37:56: end of X-cor INFO @ Fri, 10 Dec 2021 21:37:56: #2 finished! INFO @ Fri, 10 Dec 2021 21:37:56: #2 predicted fragment length is 168 bps INFO @ Fri, 10 Dec 2021 21:37:56: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 10 Dec 2021 21:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.20_model.r INFO @ Fri, 10 Dec 2021 21:37:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:37:58: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 21:37:58: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 21:37:58: #1 total tags in treatment: 10537917 INFO @ Fri, 10 Dec 2021 21:37:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:37:58: #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 21:37:58: #1 tags after filtering in treatment: 9782629 INFO @ Fri, 10 Dec 2021 21:37:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 21:37:58: #1 finished! INFO @ Fri, 10 Dec 2021 21:37:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:37:59: #2 number of paired peaks: 531 WARNING @ Fri, 10 Dec 2021 21:37:59: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Fri, 10 Dec 2021 21:37:59: start model_add_line... INFO @ Fri, 10 Dec 2021 21:37:59: start X-correlation... INFO @ Fri, 10 Dec 2021 21:37:59: end of X-cor INFO @ Fri, 10 Dec 2021 21:37:59: #2 finished! INFO @ Fri, 10 Dec 2021 21:37:59: #2 predicted fragment length is 168 bps INFO @ Fri, 10 Dec 2021 21:37:59: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 10 Dec 2021 21:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.10_model.r INFO @ Fri, 10 Dec 2021 21:37:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:38:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:38:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:38:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:38:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:38:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.20_summits.bed INFO @ Fri, 10 Dec 2021 21:38:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:38:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:38:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:38:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978876/ERX3978876.10_summits.bed INFO @ Fri, 10 Dec 2021 21:38:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3973 records, 4 fields): 9 millis CompletedMACS2peakCalling