Job ID = 16439301 SRX = SRX15206483 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:51:20 prefetch.2.10.7: 1) Downloading 'SRR19139320'... 2022-08-02T05:51:20 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:51:47 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:51:48 prefetch.2.10.7: 'SRR19139320' is valid 2022-08-02T05:51:48 prefetch.2.10.7: 1) 'SRR19139320' was downloaded successfully 2022-08-02T05:51:48 prefetch.2.10.7: 'SRR19139320' has 0 unresolved dependencies Read 8786742 spots for SRR19139320/SRR19139320.sra Written 8786742 spots for SRR19139320/SRR19139320.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439368 ("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: 00:05:00 8786742 reads; of these: 8786742 (100.00%) were unpaired; of these: 326594 (3.72%) aligned 0 times 6609398 (75.22%) aligned exactly 1 time 1850750 (21.06%) aligned >1 times 96.28% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 1843300 / 8460148 = 0.2179 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 15:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.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 15:01:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:32: 1000000 INFO @ Tue, 02 Aug 2022 15:01:44: 2000000 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 15:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.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 15:01:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:56: 3000000 INFO @ Tue, 02 Aug 2022 15:01:58: 1000000 INFO @ Tue, 02 Aug 2022 15:02:07: 2000000 INFO @ Tue, 02 Aug 2022 15:02:08: 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 15:02:16: 3000000 INFO @ Tue, 02 Aug 2022 15:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.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 15:02:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:02:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:02:19: 5000000 INFO @ Tue, 02 Aug 2022 15:02:26: 4000000 INFO @ Tue, 02 Aug 2022 15:02:29: 1000000 INFO @ Tue, 02 Aug 2022 15:02:31: 6000000 INFO @ Tue, 02 Aug 2022 15:02:36: 5000000 INFO @ Tue, 02 Aug 2022 15:02:38: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:02:38: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:02:38: #1 total tags in treatment: 6616848 INFO @ Tue, 02 Aug 2022 15:02:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:02:38: #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 15:02:38: #1 tags after filtering in treatment: 6616848 INFO @ Tue, 02 Aug 2022 15:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:02:38: #1 finished! INFO @ Tue, 02 Aug 2022 15:02:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:02:39: #2 number of paired peaks: 947 WARNING @ Tue, 02 Aug 2022 15:02:39: Fewer paired peaks (947) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 947 pairs to build model! INFO @ Tue, 02 Aug 2022 15:02:39: start model_add_line... INFO @ Tue, 02 Aug 2022 15:02:39: start X-correlation... INFO @ Tue, 02 Aug 2022 15:02:39: end of X-cor INFO @ Tue, 02 Aug 2022 15:02:39: #2 finished! INFO @ Tue, 02 Aug 2022 15:02:39: #2 predicted fragment length is 204 bps INFO @ Tue, 02 Aug 2022 15:02:39: #2 alternative fragment length(s) may be 204 bps INFO @ Tue, 02 Aug 2022 15:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.05_model.r INFO @ Tue, 02 Aug 2022 15:02:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:02:39: 2000000 INFO @ Tue, 02 Aug 2022 15:02:45: 6000000 INFO @ Tue, 02 Aug 2022 15:02:50: 3000000 INFO @ Tue, 02 Aug 2022 15:02:51: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:02:51: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:02:51: #1 total tags in treatment: 6616848 INFO @ Tue, 02 Aug 2022 15:02:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:02:51: #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 15:02:51: #1 tags after filtering in treatment: 6616848 INFO @ Tue, 02 Aug 2022 15:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:02:51: #1 finished! INFO @ Tue, 02 Aug 2022 15:02:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:02:52: #2 number of paired peaks: 947 WARNING @ Tue, 02 Aug 2022 15:02:52: Fewer paired peaks (947) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 947 pairs to build model! INFO @ Tue, 02 Aug 2022 15:02:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:02:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:02:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:02:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:02:52: #2 predicted fragment length is 204 bps INFO @ Tue, 02 Aug 2022 15:02:52: #2 alternative fragment length(s) may be 204 bps INFO @ Tue, 02 Aug 2022 15:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.10_model.r INFO @ Tue, 02 Aug 2022 15:02:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:02:59: 4000000 INFO @ Tue, 02 Aug 2022 15:03:01: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:03:09: 5000000 INFO @ Tue, 02 Aug 2022 15:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.05_summits.bed INFO @ Tue, 02 Aug 2022 15:03:13: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3079 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:03:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:03:19: 6000000 INFO @ Tue, 02 Aug 2022 15:03:25: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:03:25: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:03:25: #1 total tags in treatment: 6616848 INFO @ Tue, 02 Aug 2022 15:03:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:03:25: #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 15:03:25: #1 tags after filtering in treatment: 6616848 INFO @ Tue, 02 Aug 2022 15:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:03:25: #1 finished! INFO @ Tue, 02 Aug 2022 15:03:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:03:26: #2 number of paired peaks: 947 WARNING @ Tue, 02 Aug 2022 15:03:26: Fewer paired peaks (947) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 947 pairs to build model! INFO @ Tue, 02 Aug 2022 15:03:26: start model_add_line... INFO @ Tue, 02 Aug 2022 15:03:26: start X-correlation... INFO @ Tue, 02 Aug 2022 15:03:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:03:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:03:26: #2 predicted fragment length is 204 bps INFO @ Tue, 02 Aug 2022 15:03:26: #2 alternative fragment length(s) may be 204 bps INFO @ Tue, 02 Aug 2022 15:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.20_model.r INFO @ Tue, 02 Aug 2022 15:03:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.10_summits.bed INFO @ Tue, 02 Aug 2022 15:03:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1612 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:03:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:04:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:04:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:04:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206483/SRX15206483.20_summits.bed INFO @ Tue, 02 Aug 2022 15:04:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 21 millis CompletedMACS2peakCalling