Job ID = 16439172 SRX = SRX15206455 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:42:45 prefetch.2.10.7: 1) Downloading 'SRR19139351'... 2022-08-02T05:42:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:42:58 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:42:58 prefetch.2.10.7: 'SRR19139351' is valid 2022-08-02T05:42:58 prefetch.2.10.7: 1) 'SRR19139351' was downloaded successfully 2022-08-02T05:42:58 prefetch.2.10.7: 'SRR19139351' has 0 unresolved dependencies Read 7587875 spots for SRR19139351/SRR19139351.sra Written 7587875 spots for SRR19139351/SRR19139351.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439276 ("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 7587875 reads; of these: 7587875 (100.00%) were unpaired; of these: 380894 (5.02%) aligned 0 times 5846871 (77.06%) aligned exactly 1 time 1360110 (17.92%) aligned >1 times 94.98% 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] 653361 / 7206981 = 0.0907 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 14:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.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 14:48:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:48:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:48:36: 1000000 INFO @ Tue, 02 Aug 2022 14:48:45: 2000000 INFO @ Tue, 02 Aug 2022 14:48:53: 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 14:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.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 14:48:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:48:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:02: 4000000 INFO @ Tue, 02 Aug 2022 14:49:08: 1000000 INFO @ Tue, 02 Aug 2022 14:49:11: 5000000 INFO @ Tue, 02 Aug 2022 14:49:19: 2000000 INFO @ Tue, 02 Aug 2022 14:49:20: 6000000 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 14:49:25: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:49:25: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:49:25: #1 total tags in treatment: 6553620 INFO @ Tue, 02 Aug 2022 14:49:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:25: #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 14:49:25: #1 tags after filtering in treatment: 6553620 INFO @ Tue, 02 Aug 2022 14:49:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:26: #2 number of paired peaks: 413 WARNING @ Tue, 02 Aug 2022 14:49:26: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 02 Aug 2022 14:49:26: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:26: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:26: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:26: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:26: #2 predicted fragment length is 169 bps INFO @ Tue, 02 Aug 2022 14:49:26: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 02 Aug 2022 14:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.05_model.r INFO @ Tue, 02 Aug 2022 14:49:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.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 14:49:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:29: 3000000 INFO @ Tue, 02 Aug 2022 14:49:35: 1000000 INFO @ Tue, 02 Aug 2022 14:49:40: 4000000 INFO @ Tue, 02 Aug 2022 14:49:44: 2000000 INFO @ Tue, 02 Aug 2022 14:49:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:51: 5000000 INFO @ Tue, 02 Aug 2022 14:49:52: 3000000 INFO @ Tue, 02 Aug 2022 14:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.05_summits.bed INFO @ Tue, 02 Aug 2022 14:49:58: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2006 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:00: 4000000 INFO @ Tue, 02 Aug 2022 14:50:02: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:50:08: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:08: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:08: #1 total tags in treatment: 6553620 INFO @ Tue, 02 Aug 2022 14:50:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:08: #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 14:50:08: #1 tags after filtering in treatment: 6553620 INFO @ Tue, 02 Aug 2022 14:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:09: #2 number of paired peaks: 413 WARNING @ Tue, 02 Aug 2022 14:50:09: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:09: #2 predicted fragment length is 169 bps INFO @ Tue, 02 Aug 2022 14:50:09: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 02 Aug 2022 14:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.10_model.r INFO @ Tue, 02 Aug 2022 14:50:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:09: 5000000 INFO @ Tue, 02 Aug 2022 14:50:17: 6000000 INFO @ Tue, 02 Aug 2022 14:50:22: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:22: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:22: #1 total tags in treatment: 6553620 INFO @ Tue, 02 Aug 2022 14:50:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:22: #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 14:50:22: #1 tags after filtering in treatment: 6553620 INFO @ Tue, 02 Aug 2022 14:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:22: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:22: #2 number of paired peaks: 413 WARNING @ Tue, 02 Aug 2022 14:50:22: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:22: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:22: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:22: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:22: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:22: #2 predicted fragment length is 169 bps INFO @ Tue, 02 Aug 2022 14:50:22: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 02 Aug 2022 14:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.20_model.r INFO @ Tue, 02 Aug 2022 14:50:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:41: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (836 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206455/SRX15206455.20_summits.bed INFO @ Tue, 02 Aug 2022 14:50:54: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (231 records, 4 fields): 116 millis CompletedMACS2peakCalling