Job ID = 16439451 SRX = SRX9518313 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24698424 spots for SRR13070796/SRR13070796.sra Written 24698424 spots for SRR13070796/SRR13070796.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439775 ("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: 00:52:00 24698424 reads; of these: 24698424 (100.00%) were paired; of these: 8371917 (33.90%) aligned concordantly 0 times 8463397 (34.27%) aligned concordantly exactly 1 time 7863110 (31.84%) aligned concordantly >1 times ---- 8371917 pairs aligned concordantly 0 times; of these: 371325 (4.44%) aligned discordantly 1 time ---- 8000592 pairs aligned 0 times concordantly or discordantly; of these: 16001184 mates make up the pairs; of these: 14831297 (92.69%) aligned 0 times 331691 (2.07%) aligned exactly 1 time 838196 (5.24%) aligned >1 times 69.98% overall alignment rate Time searching: 00:52:01 Overall time: 00:52:01 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 16 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] 6206434 / 16625159 = 0.3733 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 16:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.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 16:14:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:14:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:14:30: 1000000 INFO @ Tue, 02 Aug 2022 16:14:36: 2000000 INFO @ Tue, 02 Aug 2022 16:14:41: 3000000 INFO @ Tue, 02 Aug 2022 16:14:47: 4000000 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 16:14:52: 5000000 INFO @ Tue, 02 Aug 2022 16:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.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 16:14:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:14:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:14:59: 6000000 INFO @ Tue, 02 Aug 2022 16:15:02: 1000000 INFO @ Tue, 02 Aug 2022 16:15:06: 7000000 INFO @ Tue, 02 Aug 2022 16:15:09: 2000000 INFO @ Tue, 02 Aug 2022 16:15:12: 8000000 INFO @ Tue, 02 Aug 2022 16:15:17: 3000000 INFO @ Tue, 02 Aug 2022 16:15:19: 9000000 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 16:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.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 16:15:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:15:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:15:25: 4000000 INFO @ Tue, 02 Aug 2022 16:15:26: 10000000 INFO @ Tue, 02 Aug 2022 16:15:32: 1000000 INFO @ Tue, 02 Aug 2022 16:15:33: 11000000 INFO @ Tue, 02 Aug 2022 16:15:33: 5000000 INFO @ Tue, 02 Aug 2022 16:15:40: 2000000 INFO @ Tue, 02 Aug 2022 16:15:40: 12000000 INFO @ Tue, 02 Aug 2022 16:15:41: 6000000 INFO @ Tue, 02 Aug 2022 16:15:47: 13000000 INFO @ Tue, 02 Aug 2022 16:15:48: 3000000 INFO @ Tue, 02 Aug 2022 16:15:49: 7000000 INFO @ Tue, 02 Aug 2022 16:15:54: 14000000 INFO @ Tue, 02 Aug 2022 16:15:56: 4000000 INFO @ Tue, 02 Aug 2022 16:15:57: 8000000 INFO @ Tue, 02 Aug 2022 16:16:01: 15000000 INFO @ Tue, 02 Aug 2022 16:16:04: 5000000 INFO @ Tue, 02 Aug 2022 16:16:05: 9000000 INFO @ Tue, 02 Aug 2022 16:16:08: 16000000 INFO @ Tue, 02 Aug 2022 16:16:12: 6000000 INFO @ Tue, 02 Aug 2022 16:16:13: 10000000 INFO @ Tue, 02 Aug 2022 16:16:14: 17000000 INFO @ Tue, 02 Aug 2022 16:16:20: 7000000 INFO @ Tue, 02 Aug 2022 16:16:21: 11000000 INFO @ Tue, 02 Aug 2022 16:16:21: 18000000 INFO @ Tue, 02 Aug 2022 16:16:28: 8000000 INFO @ Tue, 02 Aug 2022 16:16:28: 19000000 INFO @ Tue, 02 Aug 2022 16:16:29: 12000000 INFO @ Tue, 02 Aug 2022 16:16:35: 9000000 INFO @ Tue, 02 Aug 2022 16:16:36: 20000000 INFO @ Tue, 02 Aug 2022 16:16:37: 13000000 INFO @ Tue, 02 Aug 2022 16:16:42: 21000000 INFO @ Tue, 02 Aug 2022 16:16:43: 10000000 INFO @ Tue, 02 Aug 2022 16:16:45: 14000000 INFO @ Tue, 02 Aug 2022 16:16:49: 22000000 INFO @ Tue, 02 Aug 2022 16:16:50: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:16:50: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:16:50: #1 total tags in treatment: 10152967 INFO @ Tue, 02 Aug 2022 16:16:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:16:50: #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 16:16:51: #1 tags after filtering in treatment: 8380964 INFO @ Tue, 02 Aug 2022 16:16:51: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 02 Aug 2022 16:16:51: #1 finished! INFO @ Tue, 02 Aug 2022 16:16:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:16:51: #2 number of paired peaks: 400 WARNING @ Tue, 02 Aug 2022 16:16:51: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Tue, 02 Aug 2022 16:16:51: start model_add_line... INFO @ Tue, 02 Aug 2022 16:16:51: start X-correlation... INFO @ Tue, 02 Aug 2022 16:16:51: end of X-cor INFO @ Tue, 02 Aug 2022 16:16:51: #2 finished! INFO @ Tue, 02 Aug 2022 16:16:51: #2 predicted fragment length is 125 bps INFO @ Tue, 02 Aug 2022 16:16:51: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 02 Aug 2022 16:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.05_model.r WARNING @ Tue, 02 Aug 2022 16:16:51: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:16:51: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Tue, 02 Aug 2022 16:16:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:16:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:16:51: 11000000 INFO @ Tue, 02 Aug 2022 16:16:53: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:16:59: 12000000 INFO @ Tue, 02 Aug 2022 16:17:01: 16000000 INFO @ Tue, 02 Aug 2022 16:17:07: 13000000 INFO @ Tue, 02 Aug 2022 16:17:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:17:09: 17000000 INFO @ Tue, 02 Aug 2022 16:17:15: 14000000 INFO @ Tue, 02 Aug 2022 16:17:17: 18000000 INFO @ Tue, 02 Aug 2022 16:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.05_summits.bed INFO @ Tue, 02 Aug 2022 16:17:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4857 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:17:23: 15000000 INFO @ Tue, 02 Aug 2022 16:17:25: 19000000 INFO @ Tue, 02 Aug 2022 16:17:31: 16000000 INFO @ Tue, 02 Aug 2022 16:17:33: 20000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:17:39: 17000000 INFO @ Tue, 02 Aug 2022 16:17:41: 21000000 INFO @ Tue, 02 Aug 2022 16:17:47: 18000000 INFO @ Tue, 02 Aug 2022 16:17:49: 22000000 INFO @ Tue, 02 Aug 2022 16:17:50: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:17:50: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:17:50: #1 total tags in treatment: 10152967 INFO @ Tue, 02 Aug 2022 16:17:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:17:50: #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 16:17:50: #1 tags after filtering in treatment: 8380964 INFO @ Tue, 02 Aug 2022 16:17:50: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 02 Aug 2022 16:17:50: #1 finished! INFO @ Tue, 02 Aug 2022 16:17:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:17:51: #2 number of paired peaks: 400 WARNING @ Tue, 02 Aug 2022 16:17:51: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Tue, 02 Aug 2022 16:17:51: start model_add_line... INFO @ Tue, 02 Aug 2022 16:17:51: start X-correlation... INFO @ Tue, 02 Aug 2022 16:17:51: end of X-cor INFO @ Tue, 02 Aug 2022 16:17:51: #2 finished! INFO @ Tue, 02 Aug 2022 16:17:51: #2 predicted fragment length is 125 bps INFO @ Tue, 02 Aug 2022 16:17:51: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 02 Aug 2022 16:17:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.10_model.r WARNING @ Tue, 02 Aug 2022 16:17:51: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:17:51: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Tue, 02 Aug 2022 16:17:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:17:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:17:54: 19000000 INFO @ Tue, 02 Aug 2022 16:18:02: 20000000 INFO @ Tue, 02 Aug 2022 16:18:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:18:09: 21000000 INFO @ Tue, 02 Aug 2022 16:18:16: 22000000 INFO @ Tue, 02 Aug 2022 16:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:18:17: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:18:17: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:18:17: #1 total tags in treatment: 10152967 INFO @ Tue, 02 Aug 2022 16:18:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:18:17: #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 16:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.10_summits.bed INFO @ Tue, 02 Aug 2022 16:18:17: #1 tags after filtering in treatment: 8380964 INFO @ Tue, 02 Aug 2022 16:18:17: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 02 Aug 2022 16:18:17: #1 finished! INFO @ Tue, 02 Aug 2022 16:18:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:18:18: Done! INFO @ Tue, 02 Aug 2022 16:18:18: #2 number of paired peaks: 400 WARNING @ Tue, 02 Aug 2022 16:18:18: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Tue, 02 Aug 2022 16:18:18: start model_add_line... pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2139 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:18:18: start X-correlation... INFO @ Tue, 02 Aug 2022 16:18:18: end of X-cor INFO @ Tue, 02 Aug 2022 16:18:18: #2 finished! INFO @ Tue, 02 Aug 2022 16:18:18: #2 predicted fragment length is 125 bps INFO @ Tue, 02 Aug 2022 16:18:18: #2 alternative fragment length(s) may be 125 bps INFO @ Tue, 02 Aug 2022 16:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.20_model.r WARNING @ Tue, 02 Aug 2022 16:18:18: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:18:18: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Tue, 02 Aug 2022 16:18:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:18:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:18:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518313/SRX9518313.20_summits.bed INFO @ Tue, 02 Aug 2022 16:18:45: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (757 records, 4 fields): 20 millis CompletedMACS2peakCalling