Job ID = 16439399 SRX = SRX13453896 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9394906 spots for SRR17276242/SRR17276242.sra Written 9394906 spots for SRR17276242/SRR17276242.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439603 ("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: 00:31:31 9394906 reads; of these: 9394906 (100.00%) were paired; of these: 602754 (6.42%) aligned concordantly 0 times 6976877 (74.26%) aligned concordantly exactly 1 time 1815275 (19.32%) aligned concordantly >1 times ---- 602754 pairs aligned concordantly 0 times; of these: 228711 (37.94%) aligned discordantly 1 time ---- 374043 pairs aligned 0 times concordantly or discordantly; of these: 748086 mates make up the pairs; of these: 359275 (48.03%) aligned 0 times 220969 (29.54%) aligned exactly 1 time 167842 (22.44%) aligned >1 times 98.09% overall alignment rate Time searching: 00:31:31 Overall time: 00:31:31 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] 111552 / 8907967 = 0.0125 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 15:45:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.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 15:45:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:45:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:45:54: 1000000 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 15:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.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 15:46:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:46:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:46:09: 2000000 INFO @ Tue, 02 Aug 2022 15:46:24: 1000000 INFO @ Tue, 02 Aug 2022 15:46:24: 3000000 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 15:46:39: 2000000 INFO @ Tue, 02 Aug 2022 15:46:39: 4000000 INFO @ Tue, 02 Aug 2022 15:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.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 15:46:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:46:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:46:54: 3000000 INFO @ Tue, 02 Aug 2022 15:46:55: 5000000 INFO @ Tue, 02 Aug 2022 15:46:56: 1000000 INFO @ Tue, 02 Aug 2022 15:47:09: 4000000 INFO @ Tue, 02 Aug 2022 15:47:11: 2000000 INFO @ Tue, 02 Aug 2022 15:47:11: 6000000 INFO @ Tue, 02 Aug 2022 15:47:23: 5000000 INFO @ Tue, 02 Aug 2022 15:47:25: 3000000 INFO @ Tue, 02 Aug 2022 15:47:26: 7000000 INFO @ Tue, 02 Aug 2022 15:47:38: 6000000 INFO @ Tue, 02 Aug 2022 15:47:40: 4000000 INFO @ Tue, 02 Aug 2022 15:47:41: 8000000 INFO @ Tue, 02 Aug 2022 15:47:53: 7000000 INFO @ Tue, 02 Aug 2022 15:47:54: 5000000 INFO @ Tue, 02 Aug 2022 15:47:57: 9000000 INFO @ Tue, 02 Aug 2022 15:48:09: 8000000 INFO @ Tue, 02 Aug 2022 15:48:09: 6000000 INFO @ Tue, 02 Aug 2022 15:48:12: 10000000 INFO @ Tue, 02 Aug 2022 15:48:23: 7000000 INFO @ Tue, 02 Aug 2022 15:48:24: 9000000 INFO @ Tue, 02 Aug 2022 15:48:26: 11000000 INFO @ Tue, 02 Aug 2022 15:48:37: 8000000 INFO @ Tue, 02 Aug 2022 15:48:39: 10000000 INFO @ Tue, 02 Aug 2022 15:48:41: 12000000 INFO @ Tue, 02 Aug 2022 15:48:51: 9000000 INFO @ Tue, 02 Aug 2022 15:48:53: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:48:56: 13000000 INFO @ Tue, 02 Aug 2022 15:49:04: 10000000 INFO @ Tue, 02 Aug 2022 15:49:08: 12000000 INFO @ Tue, 02 Aug 2022 15:49:12: 14000000 INFO @ Tue, 02 Aug 2022 15:49:18: 11000000 INFO @ Tue, 02 Aug 2022 15:49:23: 13000000 INFO @ Tue, 02 Aug 2022 15:49:28: 15000000 INFO @ Tue, 02 Aug 2022 15:49:31: 12000000 INFO @ Tue, 02 Aug 2022 15:49:39: 14000000 INFO @ Tue, 02 Aug 2022 15:49:43: 16000000 INFO @ Tue, 02 Aug 2022 15:49:45: 13000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:49:54: 15000000 INFO @ Tue, 02 Aug 2022 15:49:58: 17000000 INFO @ Tue, 02 Aug 2022 15:50:00: 14000000 INFO @ Tue, 02 Aug 2022 15:50:09: 16000000 INFO @ Tue, 02 Aug 2022 15:50:13: 18000000 INFO @ Tue, 02 Aug 2022 15:50:15: 15000000 INFO @ Tue, 02 Aug 2022 15:50:16: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:50:16: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:50:16: #1 total tags in treatment: 8680720 INFO @ Tue, 02 Aug 2022 15:50:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:50:16: #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 15:50:17: #1 tags after filtering in treatment: 8414052 INFO @ Tue, 02 Aug 2022 15:50:17: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:50:17: #1 finished! INFO @ Tue, 02 Aug 2022 15:50:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:50:17: #2 number of paired peaks: 163 WARNING @ Tue, 02 Aug 2022 15:50:17: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 02 Aug 2022 15:50:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:50:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:50:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:50:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:50:17: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 15:50:17: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 15:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.05_model.r INFO @ Tue, 02 Aug 2022 15:50:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:50:23: 17000000 INFO @ Tue, 02 Aug 2022 15:50:30: 16000000 INFO @ Tue, 02 Aug 2022 15:50:37: 18000000 INFO @ Tue, 02 Aug 2022 15:50:40: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:50:40: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:50:40: #1 total tags in treatment: 8680720 INFO @ Tue, 02 Aug 2022 15:50:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:50:40: #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 15:50:40: #1 tags after filtering in treatment: 8414052 INFO @ Tue, 02 Aug 2022 15:50:40: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:50:40: #1 finished! INFO @ Tue, 02 Aug 2022 15:50:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:50:41: #2 number of paired peaks: 163 WARNING @ Tue, 02 Aug 2022 15:50:41: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 02 Aug 2022 15:50:41: start model_add_line... INFO @ Tue, 02 Aug 2022 15:50:41: start X-correlation... INFO @ Tue, 02 Aug 2022 15:50:41: end of X-cor INFO @ Tue, 02 Aug 2022 15:50:41: #2 finished! INFO @ Tue, 02 Aug 2022 15:50:41: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 15:50:41: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 15:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.10_model.r INFO @ Tue, 02 Aug 2022 15:50:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:50:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:50:44: 17000000 INFO @ Tue, 02 Aug 2022 15:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.05_summits.bed INFO @ Tue, 02 Aug 2022 15:50:57: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1674 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:50:59: 18000000 INFO @ Tue, 02 Aug 2022 15:51:01: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:51:01: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:51:01: #1 total tags in treatment: 8680720 INFO @ Tue, 02 Aug 2022 15:51:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:51:01: #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 15:51:01: #1 tags after filtering in treatment: 8414052 INFO @ Tue, 02 Aug 2022 15:51:01: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:51:01: #1 finished! INFO @ Tue, 02 Aug 2022 15:51:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:51:02: #2 number of paired peaks: 163 WARNING @ Tue, 02 Aug 2022 15:51:02: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 02 Aug 2022 15:51:02: start model_add_line... INFO @ Tue, 02 Aug 2022 15:51:02: start X-correlation... INFO @ Tue, 02 Aug 2022 15:51:02: end of X-cor INFO @ Tue, 02 Aug 2022 15:51:02: #2 finished! INFO @ Tue, 02 Aug 2022 15:51:02: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 15:51:02: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 15:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.20_model.r INFO @ Tue, 02 Aug 2022 15:51:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:51:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:51:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:51:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.10_summits.bed INFO @ Tue, 02 Aug 2022 15:51:20: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (781 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:51:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13453896/SRX13453896.20_summits.bed INFO @ Tue, 02 Aug 2022 15:51:42: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (346 records, 4 fields): 4 millis CompletedMACS2peakCalling