Job ID = 16439306 SRX = SRX15206488 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:51:32 prefetch.2.10.7: 1) Downloading 'SRR19139313'... 2022-08-02T05:51:32 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:51:43 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:51:43 prefetch.2.10.7: 'SRR19139313' is valid 2022-08-02T05:51:43 prefetch.2.10.7: 1) 'SRR19139313' was downloaded successfully 2022-08-02T05:51:43 prefetch.2.10.7: 'SRR19139313' has 0 unresolved dependencies Read 5847180 spots for SRR19139313/SRR19139313.sra Written 5847180 spots for SRR19139313/SRR19139313.sra 2022-08-02T05:52:04 prefetch.2.10.7: 1) Downloading 'SRR19139314'... 2022-08-02T05:52:04 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:17 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:18 prefetch.2.10.7: 'SRR19139314' is valid 2022-08-02T05:52:18 prefetch.2.10.7: 1) 'SRR19139314' was downloaded successfully 2022-08-02T05:52:18 prefetch.2.10.7: 'SRR19139314' has 0 unresolved dependencies Read 5847180 spots for SRR19139314/SRR19139314.sra Written 5847180 spots for SRR19139314/SRR19139314.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439361 ("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: 00:04:01 11694360 reads; of these: 11694360 (100.00%) were unpaired; of these: 469363 (4.01%) aligned 0 times 9519811 (81.41%) aligned exactly 1 time 1705186 (14.58%) aligned >1 times 95.99% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 2164942 / 11224997 = 0.1929 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 15:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.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 15:00:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:07: 1000000 INFO @ Tue, 02 Aug 2022 15:00:12: 2000000 INFO @ Tue, 02 Aug 2022 15:00:18: 3000000 INFO @ Tue, 02 Aug 2022 15:00:23: 4000000 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 15:00:29: 5000000 INFO @ Tue, 02 Aug 2022 15:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.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 15:00:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:34: 6000000 INFO @ Tue, 02 Aug 2022 15:00:36: 1000000 INFO @ Tue, 02 Aug 2022 15:00:40: 7000000 INFO @ Tue, 02 Aug 2022 15:00:42: 2000000 INFO @ Tue, 02 Aug 2022 15:00:46: 8000000 INFO @ Tue, 02 Aug 2022 15:00:48: 3000000 INFO @ Tue, 02 Aug 2022 15:00:52: 9000000 INFO @ Tue, 02 Aug 2022 15:00:52: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:00:52: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:00:52: #1 total tags in treatment: 9060055 INFO @ Tue, 02 Aug 2022 15:00:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:00:52: #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 15:00:52: #1 tags after filtering in treatment: 9060055 INFO @ Tue, 02 Aug 2022 15:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:00:52: #1 finished! INFO @ Tue, 02 Aug 2022 15:00:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:00:53: #2 number of paired peaks: 3751 INFO @ Tue, 02 Aug 2022 15:00:53: start model_add_line... INFO @ Tue, 02 Aug 2022 15:00:53: start X-correlation... INFO @ Tue, 02 Aug 2022 15:00:53: end of X-cor INFO @ Tue, 02 Aug 2022 15:00:53: #2 finished! INFO @ Tue, 02 Aug 2022 15:00:53: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 15:00:53: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 15:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.05_model.r INFO @ Tue, 02 Aug 2022 15:00:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:00:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:00:54: 4000000 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 15:01:00: 5000000 INFO @ Tue, 02 Aug 2022 15:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.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 15:01:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:05: 6000000 INFO @ Tue, 02 Aug 2022 15:01:07: 1000000 INFO @ Tue, 02 Aug 2022 15:01:12: 7000000 INFO @ Tue, 02 Aug 2022 15:01:14: 2000000 INFO @ Tue, 02 Aug 2022 15:01:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:17: 8000000 INFO @ Tue, 02 Aug 2022 15:01:21: 3000000 INFO @ Tue, 02 Aug 2022 15:01:23: 9000000 INFO @ Tue, 02 Aug 2022 15:01:24: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:01:24: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:01:24: #1 total tags in treatment: 9060055 INFO @ Tue, 02 Aug 2022 15:01:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:24: #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 15:01:24: #1 tags after filtering in treatment: 9060055 INFO @ Tue, 02 Aug 2022 15:01:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:24: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:01:25: #2 number of paired peaks: 3751 INFO @ Tue, 02 Aug 2022 15:01:25: start model_add_line... INFO @ Tue, 02 Aug 2022 15:01:25: start X-correlation... INFO @ Tue, 02 Aug 2022 15:01:25: end of X-cor INFO @ Tue, 02 Aug 2022 15:01:25: #2 finished! INFO @ Tue, 02 Aug 2022 15:01:25: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 15:01:25: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 15:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.10_model.r INFO @ Tue, 02 Aug 2022 15:01:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.05_summits.bed INFO @ Tue, 02 Aug 2022 15:01:26: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (14096 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:28: 4000000 INFO @ Tue, 02 Aug 2022 15:01:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:01:40: 6000000 INFO @ Tue, 02 Aug 2022 15:01:46: 7000000 INFO @ Tue, 02 Aug 2022 15:01:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:53: 8000000 INFO @ Tue, 02 Aug 2022 15:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.10_summits.bed INFO @ Tue, 02 Aug 2022 15:01:57: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9307 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:58: 9000000 INFO @ Tue, 02 Aug 2022 15:01:59: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:01:59: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:01:59: #1 total tags in treatment: 9060055 INFO @ Tue, 02 Aug 2022 15:01:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:59: #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 15:01:59: #1 tags after filtering in treatment: 9060055 INFO @ Tue, 02 Aug 2022 15:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:59: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:02:00: #2 number of paired peaks: 3751 INFO @ Tue, 02 Aug 2022 15:02:00: start model_add_line... INFO @ Tue, 02 Aug 2022 15:02:00: start X-correlation... INFO @ Tue, 02 Aug 2022 15:02:00: end of X-cor INFO @ Tue, 02 Aug 2022 15:02:00: #2 finished! INFO @ Tue, 02 Aug 2022 15:02:00: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 15:02:00: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 15:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.20_model.r INFO @ Tue, 02 Aug 2022 15:02:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:02:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:02:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206488/SRX15206488.20_summits.bed INFO @ Tue, 02 Aug 2022 15:02:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (5421 records, 4 fields): 23 millis CompletedMACS2peakCalling