Job ID = 16438993 SRX = SRX15206436 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:20:48 prefetch.2.10.7: 1) Downloading 'SRR19139375'... 2022-08-02T05:20:48 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:20:57 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:20:57 prefetch.2.10.7: 'SRR19139375' is valid 2022-08-02T05:20:57 prefetch.2.10.7: 1) 'SRR19139375' was downloaded successfully 2022-08-02T05:20:57 prefetch.2.10.7: 'SRR19139375' has 0 unresolved dependencies Read 5946014 spots for SRR19139375/SRR19139375.sra Written 5946014 spots for SRR19139375/SRR19139375.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439024 ("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: 00:02:25 5946014 reads; of these: 5946014 (100.00%) were unpaired; of these: 149030 (2.51%) aligned 0 times 2820540 (47.44%) aligned exactly 1 time 2976444 (50.06%) aligned >1 times 97.49% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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_rmdupse_core] 543116 / 5796984 = 0.0937 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 14:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.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 14:25:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:23: 1000000 INFO @ Tue, 02 Aug 2022 14:25:29: 2000000 INFO @ Tue, 02 Aug 2022 14:25:35: 3000000 INFO @ Tue, 02 Aug 2022 14:25:41: 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 14:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.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 14:25:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:48: 5000000 INFO @ Tue, 02 Aug 2022 14:25:49: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:25:49: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:25:49: #1 total tags in treatment: 5253868 INFO @ Tue, 02 Aug 2022 14:25:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:25:49: #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 14:25:49: #1 tags after filtering in treatment: 5253868 INFO @ Tue, 02 Aug 2022 14:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:25:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:25:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:25:50: #2 number of paired peaks: 1867 INFO @ Tue, 02 Aug 2022 14:25:50: start model_add_line... INFO @ Tue, 02 Aug 2022 14:25:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:25:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:25:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:25:50: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 14:25:50: #2 alternative fragment length(s) may be 4,220 bps INFO @ Tue, 02 Aug 2022 14:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.05_model.r INFO @ Tue, 02 Aug 2022 14:25:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:25:52: 1000000 INFO @ Tue, 02 Aug 2022 14:25:59: 2000000 INFO @ Tue, 02 Aug 2022 14:26:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:05: 3000000 INFO @ Tue, 02 Aug 2022 14:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.05_summits.bed INFO @ Tue, 02 Aug 2022 14:26:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2546 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:26:11: 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 14:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.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 14:26:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:18: 5000000 INFO @ Tue, 02 Aug 2022 14:26:19: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:26:19: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:26:19: #1 total tags in treatment: 5253868 INFO @ Tue, 02 Aug 2022 14:26:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:19: #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 14:26:19: #1 tags after filtering in treatment: 5253868 INFO @ Tue, 02 Aug 2022 14:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:26:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:20: #2 number of paired peaks: 1867 INFO @ Tue, 02 Aug 2022 14:26:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:20: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 14:26:20: #2 alternative fragment length(s) may be 4,220 bps INFO @ Tue, 02 Aug 2022 14:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.10_model.r INFO @ Tue, 02 Aug 2022 14:26:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:26:23: 1000000 INFO @ Tue, 02 Aug 2022 14:26:29: 2000000 INFO @ Tue, 02 Aug 2022 14:26:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:35: 3000000 INFO @ Tue, 02 Aug 2022 14:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.10_summits.bed INFO @ Tue, 02 Aug 2022 14:26:37: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:26:42: 4000000 INFO @ Tue, 02 Aug 2022 14:26:49: 5000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:26:50: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:26:50: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:26:50: #1 total tags in treatment: 5253868 INFO @ Tue, 02 Aug 2022 14:26:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:50: #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 14:26:51: #1 tags after filtering in treatment: 5253868 INFO @ Tue, 02 Aug 2022 14:26:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:26:51: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:51: #2 number of paired peaks: 1867 INFO @ Tue, 02 Aug 2022 14:26:51: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:51: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:51: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:51: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:51: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 14:26:51: #2 alternative fragment length(s) may be 4,220 bps INFO @ Tue, 02 Aug 2022 14:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.20_model.r INFO @ Tue, 02 Aug 2022 14:26:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206436/SRX15206436.20_summits.bed INFO @ Tue, 02 Aug 2022 14:27:08: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (337 records, 4 fields): 21 millis CompletedMACS2peakCalling