Job ID = 14168339 SRX = ERX3978853 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23957455 spots for ERR3975922/ERR3975922.sra Written 23957455 spots for ERR3975922/ERR3975922.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169618 ("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: 01:01:14 23957455 reads; of these: 23957455 (100.00%) were paired; of these: 2847907 (11.89%) aligned concordantly 0 times 16436008 (68.60%) aligned concordantly exactly 1 time 4673540 (19.51%) aligned concordantly >1 times ---- 2847907 pairs aligned concordantly 0 times; of these: 530906 (18.64%) aligned discordantly 1 time ---- 2317001 pairs aligned 0 times concordantly or discordantly; of these: 4634002 mates make up the pairs; of these: 2537777 (54.76%) aligned 0 times 1038757 (22.42%) aligned exactly 1 time 1057468 (22.82%) aligned >1 times 94.70% overall alignment rate Time searching: 01:01:14 Overall time: 01:01:14 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 20 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] 11933092 / 21510898 = 0.5547 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 18:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.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 18:54:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:54:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:54:25: 1000000 INFO @ Fri, 10 Dec 2021 18:54:31: 2000000 INFO @ Fri, 10 Dec 2021 18:54:36: 3000000 INFO @ Fri, 10 Dec 2021 18:54:42: 4000000 INFO @ Fri, 10 Dec 2021 18:54:47: 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 18:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.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 18:54:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:54:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:54:54: 6000000 INFO @ Fri, 10 Dec 2021 18:54:57: 1000000 INFO @ Fri, 10 Dec 2021 18:55:01: 7000000 INFO @ Fri, 10 Dec 2021 18:55:05: 2000000 INFO @ Fri, 10 Dec 2021 18:55:07: 8000000 INFO @ Fri, 10 Dec 2021 18:55:13: 3000000 INFO @ Fri, 10 Dec 2021 18:55:14: 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 18:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.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 18:55:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:55:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:55:21: 4000000 INFO @ Fri, 10 Dec 2021 18:55:21: 10000000 INFO @ Fri, 10 Dec 2021 18:55:27: 1000000 INFO @ Fri, 10 Dec 2021 18:55:28: 11000000 INFO @ Fri, 10 Dec 2021 18:55:28: 5000000 INFO @ Fri, 10 Dec 2021 18:55:35: 2000000 INFO @ Fri, 10 Dec 2021 18:55:35: 12000000 INFO @ Fri, 10 Dec 2021 18:55:36: 6000000 INFO @ Fri, 10 Dec 2021 18:55:42: 13000000 INFO @ Fri, 10 Dec 2021 18:55:42: 3000000 INFO @ Fri, 10 Dec 2021 18:55:44: 7000000 INFO @ Fri, 10 Dec 2021 18:55:49: 14000000 INFO @ Fri, 10 Dec 2021 18:55:50: 4000000 INFO @ Fri, 10 Dec 2021 18:55:52: 8000000 INFO @ Fri, 10 Dec 2021 18:55:56: 15000000 INFO @ Fri, 10 Dec 2021 18:55:58: 5000000 INFO @ Fri, 10 Dec 2021 18:56:00: 9000000 INFO @ Fri, 10 Dec 2021 18:56:03: 16000000 INFO @ Fri, 10 Dec 2021 18:56:06: 6000000 INFO @ Fri, 10 Dec 2021 18:56:08: 10000000 INFO @ Fri, 10 Dec 2021 18:56:11: 17000000 INFO @ Fri, 10 Dec 2021 18:56:13: 7000000 INFO @ Fri, 10 Dec 2021 18:56:16: 11000000 INFO @ Fri, 10 Dec 2021 18:56:18: 18000000 INFO @ Fri, 10 Dec 2021 18:56:21: 8000000 INFO @ Fri, 10 Dec 2021 18:56:24: 12000000 INFO @ Fri, 10 Dec 2021 18:56:25: 19000000 INFO @ Fri, 10 Dec 2021 18:56:29: 9000000 INFO @ Fri, 10 Dec 2021 18:56:32: 20000000 INFO @ Fri, 10 Dec 2021 18:56:32: 13000000 INFO @ Fri, 10 Dec 2021 18:56:36: 10000000 INFO @ Fri, 10 Dec 2021 18:56:39: 21000000 INFO @ Fri, 10 Dec 2021 18:56:40: 14000000 INFO @ Fri, 10 Dec 2021 18:56:42: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:56:42: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:56:42: #1 total tags in treatment: 9449451 INFO @ Fri, 10 Dec 2021 18:56:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:56:42: #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 18:56:43: #1 tags after filtering in treatment: 8851564 INFO @ Fri, 10 Dec 2021 18:56:43: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 18:56:43: #1 finished! INFO @ Fri, 10 Dec 2021 18:56:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:56:43: #2 number of paired peaks: 321 WARNING @ Fri, 10 Dec 2021 18:56:43: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 10 Dec 2021 18:56:43: start model_add_line... INFO @ Fri, 10 Dec 2021 18:56:43: start X-correlation... INFO @ Fri, 10 Dec 2021 18:56:43: end of X-cor INFO @ Fri, 10 Dec 2021 18:56:43: #2 finished! INFO @ Fri, 10 Dec 2021 18:56:43: #2 predicted fragment length is 153 bps INFO @ Fri, 10 Dec 2021 18:56:43: #2 alternative fragment length(s) may be 153 bps INFO @ Fri, 10 Dec 2021 18:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.05_model.r INFO @ Fri, 10 Dec 2021 18:56:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:56:44: 11000000 INFO @ Fri, 10 Dec 2021 18:56:48: 15000000 INFO @ Fri, 10 Dec 2021 18:56:52: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:56:56: 16000000 INFO @ Fri, 10 Dec 2021 18:57:01: 13000000 INFO @ Fri, 10 Dec 2021 18:57:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:57:04: 17000000 INFO @ Fri, 10 Dec 2021 18:57:09: 14000000 INFO @ Fri, 10 Dec 2021 18:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.05_summits.bed INFO @ Fri, 10 Dec 2021 18:57:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4574 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:57:13: 18000000 INFO @ Fri, 10 Dec 2021 18:57:16: 15000000 INFO @ Fri, 10 Dec 2021 18:57:21: 19000000 INFO @ Fri, 10 Dec 2021 18:57:24: 16000000 INFO @ Fri, 10 Dec 2021 18:57:29: 20000000 INFO @ Fri, 10 Dec 2021 18:57:32: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:57:37: 21000000 INFO @ Fri, 10 Dec 2021 18:57:39: 18000000 INFO @ Fri, 10 Dec 2021 18:57:41: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:57:41: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:57:41: #1 total tags in treatment: 9449451 INFO @ Fri, 10 Dec 2021 18:57:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:57:41: #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 18:57:41: #1 tags after filtering in treatment: 8851564 INFO @ Fri, 10 Dec 2021 18:57:41: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 18:57:41: #1 finished! INFO @ Fri, 10 Dec 2021 18:57:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:57:41: #2 number of paired peaks: 321 WARNING @ Fri, 10 Dec 2021 18:57:41: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 10 Dec 2021 18:57:41: start model_add_line... INFO @ Fri, 10 Dec 2021 18:57:41: start X-correlation... INFO @ Fri, 10 Dec 2021 18:57:41: end of X-cor INFO @ Fri, 10 Dec 2021 18:57:41: #2 finished! INFO @ Fri, 10 Dec 2021 18:57:41: #2 predicted fragment length is 153 bps INFO @ Fri, 10 Dec 2021 18:57:41: #2 alternative fragment length(s) may be 153 bps INFO @ Fri, 10 Dec 2021 18:57:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.10_model.r INFO @ Fri, 10 Dec 2021 18:57:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:57:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:57:47: 19000000 INFO @ Fri, 10 Dec 2021 18:57:54: 20000000 INFO @ Fri, 10 Dec 2021 18:58:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:58:01: 21000000 INFO @ Fri, 10 Dec 2021 18:58:04: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:58:04: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:58:04: #1 total tags in treatment: 9449451 INFO @ Fri, 10 Dec 2021 18:58:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:58:04: #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 18:58:04: #1 tags after filtering in treatment: 8851564 INFO @ Fri, 10 Dec 2021 18:58:04: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 18:58:04: #1 finished! INFO @ Fri, 10 Dec 2021 18:58:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:58:05: #2 number of paired peaks: 321 WARNING @ Fri, 10 Dec 2021 18:58:05: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Fri, 10 Dec 2021 18:58:05: start model_add_line... INFO @ Fri, 10 Dec 2021 18:58:05: start X-correlation... INFO @ Fri, 10 Dec 2021 18:58:05: end of X-cor INFO @ Fri, 10 Dec 2021 18:58:05: #2 finished! INFO @ Fri, 10 Dec 2021 18:58:05: #2 predicted fragment length is 153 bps INFO @ Fri, 10 Dec 2021 18:58:05: #2 alternative fragment length(s) may be 153 bps INFO @ Fri, 10 Dec 2021 18:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.20_model.r INFO @ Fri, 10 Dec 2021 18:58:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:58:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:58:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:58:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.10_summits.bed INFO @ Fri, 10 Dec 2021 18:58:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1788 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:58:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978853/ERX3978853.20_summits.bed INFO @ Fri, 10 Dec 2021 18:58:32: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (780 records, 4 fields): 3 millis CompletedMACS2peakCalling