Job ID = 16436562 SRX = SRX11638459 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:40:28 prefetch.2.10.7: 1) Downloading 'SRR15334168'... 2022-08-02T02:40:28 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:41:31 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:41:31 prefetch.2.10.7: 1) 'SRR15334168' was downloaded successfully 2022-08-02T02:41:31 prefetch.2.10.7: 'SRR15334168' has 0 unresolved dependencies Read 27919588 spots for SRR15334168/SRR15334168.sra Written 27919588 spots for SRR15334168/SRR15334168.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436821 ("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: 00:06:25 27919588 reads; of these: 27919588 (100.00%) were unpaired; of these: 2880398 (10.32%) aligned 0 times 22056848 (79.00%) aligned exactly 1 time 2982342 (10.68%) aligned >1 times 89.68% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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_sort_core] merging from 12 files... [bam_rmdupse_core] 5315292 / 25039190 = 0.2123 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 11:55:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.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 11:55:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:55:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:55:05: 1000000 INFO @ Tue, 02 Aug 2022 11:55:10: 2000000 INFO @ Tue, 02 Aug 2022 11:55:14: 3000000 INFO @ Tue, 02 Aug 2022 11:55:19: 4000000 INFO @ Tue, 02 Aug 2022 11:55:24: 5000000 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 11:55:28: 6000000 INFO @ Tue, 02 Aug 2022 11:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.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 11:55:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:55:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:55:33: 7000000 INFO @ Tue, 02 Aug 2022 11:55:36: 1000000 INFO @ Tue, 02 Aug 2022 11:55:38: 8000000 INFO @ Tue, 02 Aug 2022 11:55:42: 2000000 INFO @ Tue, 02 Aug 2022 11:55:43: 9000000 INFO @ Tue, 02 Aug 2022 11:55:48: 3000000 INFO @ Tue, 02 Aug 2022 11:55:48: 10000000 INFO @ Tue, 02 Aug 2022 11:55:53: 11000000 INFO @ Tue, 02 Aug 2022 11:55:54: 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 11:55:58: 12000000 INFO @ Tue, 02 Aug 2022 11:56:00: 5000000 INFO @ Tue, 02 Aug 2022 11:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.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 11:56:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:56:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:56:03: 13000000 INFO @ Tue, 02 Aug 2022 11:56:05: 1000000 INFO @ Tue, 02 Aug 2022 11:56:05: 6000000 INFO @ Tue, 02 Aug 2022 11:56:08: 14000000 INFO @ Tue, 02 Aug 2022 11:56:10: 2000000 INFO @ Tue, 02 Aug 2022 11:56:11: 7000000 INFO @ Tue, 02 Aug 2022 11:56:13: 15000000 INFO @ Tue, 02 Aug 2022 11:56:16: 3000000 INFO @ Tue, 02 Aug 2022 11:56:17: 8000000 INFO @ Tue, 02 Aug 2022 11:56:18: 16000000 INFO @ Tue, 02 Aug 2022 11:56:21: 4000000 INFO @ Tue, 02 Aug 2022 11:56:23: 9000000 INFO @ Tue, 02 Aug 2022 11:56:23: 17000000 INFO @ Tue, 02 Aug 2022 11:56:26: 5000000 INFO @ Tue, 02 Aug 2022 11:56:28: 18000000 INFO @ Tue, 02 Aug 2022 11:56:29: 10000000 INFO @ Tue, 02 Aug 2022 11:56:31: 6000000 INFO @ Tue, 02 Aug 2022 11:56:33: 19000000 INFO @ Tue, 02 Aug 2022 11:56:35: 11000000 INFO @ Tue, 02 Aug 2022 11:56:36: 7000000 INFO @ Tue, 02 Aug 2022 11:56:37: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:56:37: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:56:37: #1 total tags in treatment: 19723898 INFO @ Tue, 02 Aug 2022 11:56:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:56:37: #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 11:56:37: #1 tags after filtering in treatment: 19723898 INFO @ Tue, 02 Aug 2022 11:56:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:56:37: #1 finished! INFO @ Tue, 02 Aug 2022 11:56:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:56:38: #2 number of paired peaks: 839 WARNING @ Tue, 02 Aug 2022 11:56:38: Fewer paired peaks (839) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 839 pairs to build model! INFO @ Tue, 02 Aug 2022 11:56:38: start model_add_line... INFO @ Tue, 02 Aug 2022 11:56:39: start X-correlation... INFO @ Tue, 02 Aug 2022 11:56:39: end of X-cor INFO @ Tue, 02 Aug 2022 11:56:39: #2 finished! INFO @ Tue, 02 Aug 2022 11:56:39: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 11:56:39: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 11:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.05_model.r INFO @ Tue, 02 Aug 2022 11:56:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:56:40: 12000000 INFO @ Tue, 02 Aug 2022 11:56:41: 8000000 INFO @ Tue, 02 Aug 2022 11:56:46: 13000000 INFO @ Tue, 02 Aug 2022 11:56:46: 9000000 INFO @ Tue, 02 Aug 2022 11:56:51: 10000000 INFO @ Tue, 02 Aug 2022 11:56:52: 14000000 INFO @ Tue, 02 Aug 2022 11:56:56: 11000000 INFO @ Tue, 02 Aug 2022 11:56:57: 15000000 INFO @ Tue, 02 Aug 2022 11:57:01: 12000000 INFO @ Tue, 02 Aug 2022 11:57:03: 16000000 INFO @ Tue, 02 Aug 2022 11:57:06: 13000000 INFO @ Tue, 02 Aug 2022 11:57:09: 17000000 INFO @ Tue, 02 Aug 2022 11:57:12: 14000000 INFO @ Tue, 02 Aug 2022 11:57:15: 18000000 INFO @ Tue, 02 Aug 2022 11:57:17: 15000000 INFO @ Tue, 02 Aug 2022 11:57:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:57:20: 19000000 INFO @ Tue, 02 Aug 2022 11:57:22: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:57:24: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:57:24: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:57:24: #1 total tags in treatment: 19723898 INFO @ Tue, 02 Aug 2022 11:57:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:57:24: #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 11:57:25: #1 tags after filtering in treatment: 19723898 INFO @ Tue, 02 Aug 2022 11:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:57:25: #1 finished! INFO @ Tue, 02 Aug 2022 11:57:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:57:26: #2 number of paired peaks: 839 WARNING @ Tue, 02 Aug 2022 11:57:26: Fewer paired peaks (839) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 839 pairs to build model! INFO @ Tue, 02 Aug 2022 11:57:26: start model_add_line... INFO @ Tue, 02 Aug 2022 11:57:26: start X-correlation... INFO @ Tue, 02 Aug 2022 11:57:26: end of X-cor INFO @ Tue, 02 Aug 2022 11:57:26: #2 finished! INFO @ Tue, 02 Aug 2022 11:57:26: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 11:57:26: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 11:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.10_model.r INFO @ Tue, 02 Aug 2022 11:57:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:57:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:57:28: 17000000 INFO @ Tue, 02 Aug 2022 11:57:34: 18000000 INFO @ Tue, 02 Aug 2022 11:57:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:57:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:57:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.05_summits.bed INFO @ Tue, 02 Aug 2022 11:57:39: Done! INFO @ Tue, 02 Aug 2022 11:57:39: 19000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11609 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:57:43: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:57:43: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:57:43: #1 total tags in treatment: 19723898 INFO @ Tue, 02 Aug 2022 11:57:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:57:43: #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 11:57:43: #1 tags after filtering in treatment: 19723898 INFO @ Tue, 02 Aug 2022 11:57:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:57:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:57:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:57:45: #2 number of paired peaks: 839 WARNING @ Tue, 02 Aug 2022 11:57:45: Fewer paired peaks (839) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 839 pairs to build model! INFO @ Tue, 02 Aug 2022 11:57:45: start model_add_line... INFO @ Tue, 02 Aug 2022 11:57:45: start X-correlation... INFO @ Tue, 02 Aug 2022 11:57:45: end of X-cor INFO @ Tue, 02 Aug 2022 11:57:45: #2 finished! INFO @ Tue, 02 Aug 2022 11:57:45: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 11:57:45: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 11:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.20_model.r INFO @ Tue, 02 Aug 2022 11:57:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:57:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:58:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.10_summits.bed INFO @ Tue, 02 Aug 2022 11:58:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7789 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638459/SRX11638459.20_summits.bed INFO @ Tue, 02 Aug 2022 11:58:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4344 records, 4 fields): 53 millis CompletedMACS2peakCalling