Job ID = 16439752 SRX = SRX14894241 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:06:03 prefetch.2.10.7: 1) Downloading 'SRR18795780'... 2022-08-02T07:06:03 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:07:03 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:07:03 prefetch.2.10.7: 1) 'SRR18795780' was downloaded successfully 2022-08-02T07:07:03 prefetch.2.10.7: 'SRR18795780' has 0 unresolved dependencies Read 49696020 spots for SRR18795780/SRR18795780.sra Written 49696020 spots for SRR18795780/SRR18795780.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439856 ("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: 00:09:11 49696020 reads; of these: 49696020 (100.00%) were unpaired; of these: 20942783 (42.14%) aligned 0 times 23007062 (46.30%) aligned exactly 1 time 5746175 (11.56%) aligned >1 times 57.86% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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] 17942455 / 28753237 = 0.6240 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 16:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.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 16:23:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:28: 1000000 INFO @ Tue, 02 Aug 2022 16:23:33: 2000000 INFO @ Tue, 02 Aug 2022 16:23:37: 3000000 INFO @ Tue, 02 Aug 2022 16:23:42: 4000000 INFO @ Tue, 02 Aug 2022 16:23:47: 5000000 INFO @ Tue, 02 Aug 2022 16:23:51: 6000000 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 16:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.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 16:23:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:56: 7000000 INFO @ Tue, 02 Aug 2022 16:23:58: 1000000 INFO @ Tue, 02 Aug 2022 16:24:01: 8000000 INFO @ Tue, 02 Aug 2022 16:24:03: 2000000 INFO @ Tue, 02 Aug 2022 16:24:06: 9000000 INFO @ Tue, 02 Aug 2022 16:24:07: 3000000 INFO @ Tue, 02 Aug 2022 16:24:10: 10000000 INFO @ Tue, 02 Aug 2022 16:24:12: 4000000 INFO @ Tue, 02 Aug 2022 16:24:14: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:24:14: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:24:14: #1 total tags in treatment: 10810782 INFO @ Tue, 02 Aug 2022 16:24:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:24:14: #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 16:24:14: #1 tags after filtering in treatment: 10810782 INFO @ Tue, 02 Aug 2022 16:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:24:14: #1 finished! INFO @ Tue, 02 Aug 2022 16:24:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:24:15: #2 number of paired peaks: 3480 INFO @ Tue, 02 Aug 2022 16:24:15: start model_add_line... INFO @ Tue, 02 Aug 2022 16:24:15: start X-correlation... INFO @ Tue, 02 Aug 2022 16:24:15: end of X-cor INFO @ Tue, 02 Aug 2022 16:24:15: #2 finished! INFO @ Tue, 02 Aug 2022 16:24:15: #2 predicted fragment length is 231 bps INFO @ Tue, 02 Aug 2022 16:24:15: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 02 Aug 2022 16:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.05_model.r INFO @ Tue, 02 Aug 2022 16:24:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:24:16: 5000000 INFO @ Tue, 02 Aug 2022 16:24:21: 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 16:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.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 16:24:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:24:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:24:25: 7000000 INFO @ Tue, 02 Aug 2022 16:24:28: 1000000 INFO @ Tue, 02 Aug 2022 16:24:30: 8000000 INFO @ Tue, 02 Aug 2022 16:24:33: 2000000 INFO @ Tue, 02 Aug 2022 16:24:34: 9000000 INFO @ Tue, 02 Aug 2022 16:24:37: 3000000 INFO @ Tue, 02 Aug 2022 16:24:39: 10000000 INFO @ Tue, 02 Aug 2022 16:24:42: 4000000 INFO @ Tue, 02 Aug 2022 16:24:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:24:43: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:24:43: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:24:43: #1 total tags in treatment: 10810782 INFO @ Tue, 02 Aug 2022 16:24:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:24:43: #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 16:24:43: #1 tags after filtering in treatment: 10810782 INFO @ Tue, 02 Aug 2022 16:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:24:43: #1 finished! INFO @ Tue, 02 Aug 2022 16:24:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:24:44: #2 number of paired peaks: 3480 INFO @ Tue, 02 Aug 2022 16:24:44: start model_add_line... INFO @ Tue, 02 Aug 2022 16:24:44: start X-correlation... INFO @ Tue, 02 Aug 2022 16:24:44: end of X-cor INFO @ Tue, 02 Aug 2022 16:24:44: #2 finished! INFO @ Tue, 02 Aug 2022 16:24:44: #2 predicted fragment length is 231 bps INFO @ Tue, 02 Aug 2022 16:24:44: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 02 Aug 2022 16:24:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.10_model.r INFO @ Tue, 02 Aug 2022 16:24:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:24:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:24:46: 5000000 INFO @ Tue, 02 Aug 2022 16:24:50: 6000000 INFO @ Tue, 02 Aug 2022 16:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.05_summits.bed INFO @ Tue, 02 Aug 2022 16:24:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6570 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:24:55: 7000000 INFO @ Tue, 02 Aug 2022 16:24:59: 8000000 INFO @ Tue, 02 Aug 2022 16:25:04: 9000000 INFO @ Tue, 02 Aug 2022 16:25:08: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:25:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:12: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:25:12: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:25:12: #1 total tags in treatment: 10810782 INFO @ Tue, 02 Aug 2022 16:25:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:12: #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 16:25:12: #1 tags after filtering in treatment: 10810782 INFO @ Tue, 02 Aug 2022 16:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:25:12: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:13: #2 number of paired peaks: 3480 INFO @ Tue, 02 Aug 2022 16:25:13: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:13: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:13: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:13: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:13: #2 predicted fragment length is 231 bps INFO @ Tue, 02 Aug 2022 16:25:13: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 02 Aug 2022 16:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.20_model.r INFO @ Tue, 02 Aug 2022 16:25:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.10_summits.bed INFO @ Tue, 02 Aug 2022 16:25:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5304 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:25:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894241/SRX14894241.20_summits.bed INFO @ Tue, 02 Aug 2022 16:25:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4098 records, 4 fields): 25 millis CompletedMACS2peakCalling