Job ID = 16439300 SRX = SRX15206482 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:51:20 prefetch.2.10.7: 1) Downloading 'SRR19139321'... 2022-08-02T05:51:21 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:51:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:51:43 prefetch.2.10.7: 'SRR19139321' is valid 2022-08-02T05:51:43 prefetch.2.10.7: 1) 'SRR19139321' was downloaded successfully 2022-08-02T05:51:43 prefetch.2.10.7: 'SRR19139321' has 0 unresolved dependencies Read 18135173 spots for SRR19139321/SRR19139321.sra Written 18135173 spots for SRR19139321/SRR19139321.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439385 ("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: 00:06:58 18135173 reads; of these: 18135173 (100.00%) were unpaired; of these: 1955957 (10.79%) aligned 0 times 12921161 (71.25%) aligned exactly 1 time 3258055 (17.97%) aligned >1 times 89.21% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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 8 files... [bam_rmdupse_core] 6882365 / 16179216 = 0.4254 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.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 @ Tue, 02 Aug 2022 15:04:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:04:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:33: 1000000 INFO @ Tue, 02 Aug 2022 15:04:41: 2000000 INFO @ Tue, 02 Aug 2022 15:04:50: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.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 @ Tue, 02 Aug 2022 15:04:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:04:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:59: 4000000 INFO @ Tue, 02 Aug 2022 15:05:05: 1000000 INFO @ Tue, 02 Aug 2022 15:05:08: 5000000 INFO @ Tue, 02 Aug 2022 15:05:13: 2000000 INFO @ Tue, 02 Aug 2022 15:05:17: 6000000 INFO @ Tue, 02 Aug 2022 15:05:22: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:05:25: 7000000 INFO @ Tue, 02 Aug 2022 15:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.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 @ Tue, 02 Aug 2022 15:05:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:05:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:05:31: 4000000 INFO @ Tue, 02 Aug 2022 15:05:33: 8000000 INFO @ Tue, 02 Aug 2022 15:05:35: 1000000 INFO @ Tue, 02 Aug 2022 15:05:41: 5000000 INFO @ Tue, 02 Aug 2022 15:05:42: 9000000 INFO @ Tue, 02 Aug 2022 15:05:44: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:05:44: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:05:44: #1 total tags in treatment: 9296851 INFO @ Tue, 02 Aug 2022 15:05:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:05:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:05:44: #1 tags after filtering in treatment: 9296851 INFO @ Tue, 02 Aug 2022 15:05:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:05:44: #1 finished! INFO @ Tue, 02 Aug 2022 15:05:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:05:45: #2 number of paired peaks: 737 WARNING @ Tue, 02 Aug 2022 15:05:45: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 02 Aug 2022 15:05:45: start model_add_line... INFO @ Tue, 02 Aug 2022 15:05:45: start X-correlation... INFO @ Tue, 02 Aug 2022 15:05:46: end of X-cor INFO @ Tue, 02 Aug 2022 15:05:46: #2 finished! INFO @ Tue, 02 Aug 2022 15:05:46: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 15:05:46: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 15:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.05_model.r INFO @ Tue, 02 Aug 2022 15:05:46: 2000000 INFO @ Tue, 02 Aug 2022 15:05:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:05:50: 6000000 INFO @ Tue, 02 Aug 2022 15:05:56: 3000000 INFO @ Tue, 02 Aug 2022 15:05:59: 7000000 INFO @ Tue, 02 Aug 2022 15:06:06: 4000000 INFO @ Tue, 02 Aug 2022 15:06:07: 8000000 INFO @ Tue, 02 Aug 2022 15:06:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:06:16: 9000000 INFO @ Tue, 02 Aug 2022 15:06:16: 5000000 INFO @ Tue, 02 Aug 2022 15:06:19: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:06:19: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:06:19: #1 total tags in treatment: 9296851 INFO @ Tue, 02 Aug 2022 15:06:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:06:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:06:19: #1 tags after filtering in treatment: 9296851 INFO @ Tue, 02 Aug 2022 15:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:06:19: #1 finished! INFO @ Tue, 02 Aug 2022 15:06:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:06:20: #2 number of paired peaks: 737 WARNING @ Tue, 02 Aug 2022 15:06:20: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 02 Aug 2022 15:06:20: start model_add_line... INFO @ Tue, 02 Aug 2022 15:06:20: start X-correlation... INFO @ Tue, 02 Aug 2022 15:06:20: end of X-cor INFO @ Tue, 02 Aug 2022 15:06:20: #2 finished! INFO @ Tue, 02 Aug 2022 15:06:20: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 15:06:20: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 15:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.10_model.r INFO @ Tue, 02 Aug 2022 15:06:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:06:26: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.05_summits.bed INFO @ Tue, 02 Aug 2022 15:06:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3259 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:06:37: 7000000 INFO @ Tue, 02 Aug 2022 15:06:47: 8000000 INFO @ Tue, 02 Aug 2022 15:06:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:06:58: 9000000 INFO @ Tue, 02 Aug 2022 15:07:00: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:07:00: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:07:00: #1 total tags in treatment: 9296851 INFO @ Tue, 02 Aug 2022 15:07:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:07:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:07:01: #1 tags after filtering in treatment: 9296851 INFO @ Tue, 02 Aug 2022 15:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:07:01: #1 finished! INFO @ Tue, 02 Aug 2022 15:07:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:07:02: #2 number of paired peaks: 737 WARNING @ Tue, 02 Aug 2022 15:07:02: Fewer paired peaks (737) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 737 pairs to build model! INFO @ Tue, 02 Aug 2022 15:07:02: start model_add_line... INFO @ Tue, 02 Aug 2022 15:07:02: start X-correlation... INFO @ Tue, 02 Aug 2022 15:07:02: end of X-cor INFO @ Tue, 02 Aug 2022 15:07:02: #2 finished! INFO @ Tue, 02 Aug 2022 15:07:02: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 15:07:02: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 15:07:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.20_model.r INFO @ Tue, 02 Aug 2022 15:07:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:07:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:07:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:07:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:07:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.10_summits.bed INFO @ Tue, 02 Aug 2022 15:07:05: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1734 records, 4 fields): 71 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:07:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:07:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:07:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:07:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206482/SRX15206482.20_summits.bed INFO @ Tue, 02 Aug 2022 15:07:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 24 millis CompletedMACS2peakCalling