Job ID = 16439188 SRX = SRX15206465 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:44:02 prefetch.2.10.7: 1) Downloading 'SRR19139341'... 2022-08-02T05:44:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:44:11 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:44:11 prefetch.2.10.7: 'SRR19139341' is valid 2022-08-02T05:44:11 prefetch.2.10.7: 1) 'SRR19139341' was downloaded successfully 2022-08-02T05:44:11 prefetch.2.10.7: 'SRR19139341' has 0 unresolved dependencies Read 7192302 spots for SRR19139341/SRR19139341.sra Written 7192302 spots for SRR19139341/SRR19139341.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439285 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:09 7192302 reads; of these: 7192302 (100.00%) were unpaired; of these: 151971 (2.11%) aligned 0 times 2751800 (38.26%) aligned exactly 1 time 4288531 (59.63%) aligned >1 times 97.89% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 998582 / 7040331 = 0.1418 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 14:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.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 14:50:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:24: 1000000 INFO @ Tue, 02 Aug 2022 14:50:32: 2000000 INFO @ Tue, 02 Aug 2022 14:50:40: 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 14:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.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 14:50:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:48: 4000000 INFO @ Tue, 02 Aug 2022 14:50:53: 1000000 INFO @ Tue, 02 Aug 2022 14:50:56: 5000000 INFO @ Tue, 02 Aug 2022 14:51:01: 2000000 INFO @ Tue, 02 Aug 2022 14:51:04: 6000000 INFO @ Tue, 02 Aug 2022 14:51:04: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:51:04: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:51:04: #1 total tags in treatment: 6041749 INFO @ Tue, 02 Aug 2022 14:51:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:04: #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 14:51:04: #1 tags after filtering in treatment: 6041749 INFO @ Tue, 02 Aug 2022 14:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:05: #2 number of paired peaks: 6003 INFO @ Tue, 02 Aug 2022 14:51:05: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:05: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:05: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:05: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:05: #2 predicted fragment length is 228 bps INFO @ Tue, 02 Aug 2022 14:51:05: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 02 Aug 2022 14:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.05_model.r INFO @ Tue, 02 Aug 2022 14:51:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:51:09: 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 14:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.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 14:51:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:51:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:17: 4000000 INFO @ Tue, 02 Aug 2022 14:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:25: 1000000 INFO @ Tue, 02 Aug 2022 14:51:26: 5000000 INFO @ Tue, 02 Aug 2022 14:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.05_summits.bed INFO @ Tue, 02 Aug 2022 14:51:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9569 records, 4 fields): 447 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:34: 2000000 INFO @ Tue, 02 Aug 2022 14:51:35: 6000000 INFO @ Tue, 02 Aug 2022 14:51:35: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:51:35: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:51:35: #1 total tags in treatment: 6041749 INFO @ Tue, 02 Aug 2022 14:51:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:35: #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 14:51:35: #1 tags after filtering in treatment: 6041749 INFO @ Tue, 02 Aug 2022 14:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:35: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:36: #2 number of paired peaks: 6003 INFO @ Tue, 02 Aug 2022 14:51:36: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:36: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:36: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:36: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:36: #2 predicted fragment length is 228 bps INFO @ Tue, 02 Aug 2022 14:51:36: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 02 Aug 2022 14:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.10_model.r INFO @ Tue, 02 Aug 2022 14:51:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:51:42: 3000000 INFO @ Tue, 02 Aug 2022 14:51:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:51:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:59: 5000000 INFO @ Tue, 02 Aug 2022 14:52:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.10_summits.bed INFO @ Tue, 02 Aug 2022 14:52:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4755 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:52:06: 6000000 INFO @ Tue, 02 Aug 2022 14:52:07: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:52:07: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:52:07: #1 total tags in treatment: 6041749 INFO @ Tue, 02 Aug 2022 14:52:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:52:07: #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 14:52:07: #1 tags after filtering in treatment: 6041749 INFO @ Tue, 02 Aug 2022 14:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:52:07: #1 finished! INFO @ Tue, 02 Aug 2022 14:52:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:52:08: #2 number of paired peaks: 6003 INFO @ Tue, 02 Aug 2022 14:52:08: start model_add_line... INFO @ Tue, 02 Aug 2022 14:52:08: start X-correlation... INFO @ Tue, 02 Aug 2022 14:52:08: end of X-cor INFO @ Tue, 02 Aug 2022 14:52:08: #2 finished! INFO @ Tue, 02 Aug 2022 14:52:08: #2 predicted fragment length is 228 bps INFO @ Tue, 02 Aug 2022 14:52:08: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 02 Aug 2022 14:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.20_model.r INFO @ Tue, 02 Aug 2022 14:52:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:52:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:52:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206465/SRX15206465.20_summits.bed INFO @ Tue, 02 Aug 2022 14:52:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1581 records, 4 fields): 14 millis CompletedMACS2peakCalling