Job ID = 16439391 SRX = SRX13453892 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7804958 spots for SRR17276246/SRR17276246.sra Written 7804958 spots for SRR17276246/SRR17276246.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439536 ("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: 00:23:26 7804958 reads; of these: 7804958 (100.00%) were paired; of these: 407618 (5.22%) aligned concordantly 0 times 5770751 (73.94%) aligned concordantly exactly 1 time 1626589 (20.84%) aligned concordantly >1 times ---- 407618 pairs aligned concordantly 0 times; of these: 123671 (30.34%) aligned discordantly 1 time ---- 283947 pairs aligned 0 times concordantly or discordantly; of these: 567894 mates make up the pairs; of these: 271244 (47.76%) aligned 0 times 169115 (29.78%) aligned exactly 1 time 127535 (22.46%) aligned >1 times 98.26% overall alignment rate Time searching: 00:23:26 Overall time: 00:23:27 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 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 147014 / 7487073 = 0.0196 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 15:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.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 15:34:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:34:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:34:36: 1000000 INFO @ Tue, 02 Aug 2022 15:34:47: 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 15:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.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 15:34:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:34:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:34:57: 3000000 INFO @ Tue, 02 Aug 2022 15:35:06: 4000000 INFO @ Tue, 02 Aug 2022 15:35:07: 1000000 INFO @ Tue, 02 Aug 2022 15:35:16: 5000000 INFO @ Tue, 02 Aug 2022 15:35:18: 2000000 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 15:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.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 15:35:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:35:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:35:26: 6000000 INFO @ Tue, 02 Aug 2022 15:35:30: 3000000 INFO @ Tue, 02 Aug 2022 15:35:36: 7000000 INFO @ Tue, 02 Aug 2022 15:35:36: 1000000 INFO @ Tue, 02 Aug 2022 15:35:41: 4000000 INFO @ Tue, 02 Aug 2022 15:35:45: 8000000 INFO @ Tue, 02 Aug 2022 15:35:46: 2000000 INFO @ Tue, 02 Aug 2022 15:35:52: 5000000 INFO @ Tue, 02 Aug 2022 15:35:55: 3000000 INFO @ Tue, 02 Aug 2022 15:35:56: 9000000 INFO @ Tue, 02 Aug 2022 15:36:02: 6000000 INFO @ Tue, 02 Aug 2022 15:36:05: 4000000 INFO @ Tue, 02 Aug 2022 15:36:06: 10000000 INFO @ Tue, 02 Aug 2022 15:36:13: 7000000 INFO @ Tue, 02 Aug 2022 15:36:14: 5000000 INFO @ Tue, 02 Aug 2022 15:36:15: 11000000 INFO @ Tue, 02 Aug 2022 15:36:23: 8000000 INFO @ Tue, 02 Aug 2022 15:36:24: 6000000 INFO @ Tue, 02 Aug 2022 15:36:26: 12000000 INFO @ Tue, 02 Aug 2022 15:36:33: 9000000 INFO @ Tue, 02 Aug 2022 15:36:34: 7000000 INFO @ Tue, 02 Aug 2022 15:36:37: 13000000 INFO @ Tue, 02 Aug 2022 15:36:44: 8000000 INFO @ Tue, 02 Aug 2022 15:36:44: 10000000 INFO @ Tue, 02 Aug 2022 15:36:47: 14000000 INFO @ Tue, 02 Aug 2022 15:36:53: 9000000 INFO @ Tue, 02 Aug 2022 15:36:55: 11000000 INFO @ Tue, 02 Aug 2022 15:36:58: 15000000 INFO @ Tue, 02 Aug 2022 15:36:58: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:36:58: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:36:58: #1 total tags in treatment: 7250358 INFO @ Tue, 02 Aug 2022 15:36:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:36:58: #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 15:36:58: #1 tags after filtering in treatment: 7024472 INFO @ Tue, 02 Aug 2022 15:36:58: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:36:58: #1 finished! INFO @ Tue, 02 Aug 2022 15:36:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:36:59: #2 number of paired peaks: 146 WARNING @ Tue, 02 Aug 2022 15:36:59: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 02 Aug 2022 15:36:59: start model_add_line... INFO @ Tue, 02 Aug 2022 15:36:59: start X-correlation... INFO @ Tue, 02 Aug 2022 15:36:59: end of X-cor INFO @ Tue, 02 Aug 2022 15:36:59: #2 finished! INFO @ Tue, 02 Aug 2022 15:36:59: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 15:36:59: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 02 Aug 2022 15:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.05_model.r INFO @ Tue, 02 Aug 2022 15:36:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:37:03: 10000000 INFO @ Tue, 02 Aug 2022 15:37:06: 12000000 INFO @ Tue, 02 Aug 2022 15:37:12: 11000000 INFO @ Tue, 02 Aug 2022 15:37:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:37:16: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.05_summits.bed INFO @ Tue, 02 Aug 2022 15:37:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1767 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:37:22: 12000000 INFO @ Tue, 02 Aug 2022 15:37:27: 14000000 INFO @ Tue, 02 Aug 2022 15:37:32: 13000000 INFO @ Tue, 02 Aug 2022 15:37:37: 15000000 INFO @ Tue, 02 Aug 2022 15:37:37: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:37:37: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:37:37: #1 total tags in treatment: 7250358 INFO @ Tue, 02 Aug 2022 15:37:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:37:37: #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 15:37:37: #1 tags after filtering in treatment: 7024472 INFO @ Tue, 02 Aug 2022 15:37:37: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:37:37: #1 finished! INFO @ Tue, 02 Aug 2022 15:37:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:37:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:37:38: #2 number of paired peaks: 146 WARNING @ Tue, 02 Aug 2022 15:37:38: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 02 Aug 2022 15:37:38: start model_add_line... INFO @ Tue, 02 Aug 2022 15:37:38: start X-correlation... INFO @ Tue, 02 Aug 2022 15:37:38: end of X-cor INFO @ Tue, 02 Aug 2022 15:37:38: #2 finished! INFO @ Tue, 02 Aug 2022 15:37:38: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 15:37:38: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 02 Aug 2022 15:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.10_model.r INFO @ Tue, 02 Aug 2022 15:37:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:37:41: 14000000 INFO @ Tue, 02 Aug 2022 15:37:51: 15000000 INFO @ Tue, 02 Aug 2022 15:37:51: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:37:51: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:37:51: #1 total tags in treatment: 7250358 INFO @ Tue, 02 Aug 2022 15:37:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:37:51: #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 15:37:51: #1 tags after filtering in treatment: 7024472 INFO @ Tue, 02 Aug 2022 15:37:51: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:37:51: #1 finished! INFO @ Tue, 02 Aug 2022 15:37:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:37:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:37:52: #2 number of paired peaks: 146 WARNING @ Tue, 02 Aug 2022 15:37:52: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Tue, 02 Aug 2022 15:37:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:37:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:37:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:37:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:37:52: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 15:37:52: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 02 Aug 2022 15:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.20_model.r INFO @ Tue, 02 Aug 2022 15:37:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:37:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.10_summits.bed INFO @ Tue, 02 Aug 2022 15:37:59: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (682 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:38:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453892/SRX13453892.20_summits.bed INFO @ Tue, 02 Aug 2022 15:38:13: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (288 records, 4 fields): 25 millis CompletedMACS2peakCalling