Job ID = 12265360 SRX = SRX6430373 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22437430 spots for SRR9669868/SRR9669868.sra Written 22437430 spots for SRR9669868/SRR9669868.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265526 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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_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] 2117234 / 12397385 = 0.1708 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.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 @ Sat, 03 Apr 2021 07:04:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:04:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:04:44: 1000000 INFO @ Sat, 03 Apr 2021 07:04:49: 2000000 INFO @ Sat, 03 Apr 2021 07:04:54: 3000000 INFO @ Sat, 03 Apr 2021 07:04:59: 4000000 INFO @ Sat, 03 Apr 2021 07:05:04: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:05:09: 6000000 INFO @ Sat, 03 Apr 2021 07:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.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 @ Sat, 03 Apr 2021 07:05:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:05:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:05:14: 7000000 INFO @ Sat, 03 Apr 2021 07:05:15: 1000000 INFO @ Sat, 03 Apr 2021 07:05:20: 8000000 INFO @ Sat, 03 Apr 2021 07:05:21: 2000000 INFO @ Sat, 03 Apr 2021 07:05:26: 9000000 INFO @ Sat, 03 Apr 2021 07:05:28: 3000000 INFO @ Sat, 03 Apr 2021 07:05:31: 10000000 INFO @ Sat, 03 Apr 2021 07:05:34: 4000000 INFO @ Sat, 03 Apr 2021 07:05:37: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.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 @ Sat, 03 Apr 2021 07:05:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:05:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:05:40: 5000000 INFO @ Sat, 03 Apr 2021 07:05:42: 12000000 INFO @ Sat, 03 Apr 2021 07:05:46: 1000000 INFO @ Sat, 03 Apr 2021 07:05:46: 6000000 INFO @ Sat, 03 Apr 2021 07:05:48: 13000000 INFO @ Sat, 03 Apr 2021 07:05:52: 2000000 INFO @ Sat, 03 Apr 2021 07:05:52: 7000000 INFO @ Sat, 03 Apr 2021 07:05:53: 14000000 INFO @ Sat, 03 Apr 2021 07:05:58: 8000000 INFO @ Sat, 03 Apr 2021 07:05:58: 3000000 INFO @ Sat, 03 Apr 2021 07:05:59: 15000000 INFO @ Sat, 03 Apr 2021 07:06:04: 16000000 INFO @ Sat, 03 Apr 2021 07:06:04: 9000000 INFO @ Sat, 03 Apr 2021 07:06:04: 4000000 INFO @ Sat, 03 Apr 2021 07:06:09: 17000000 INFO @ Sat, 03 Apr 2021 07:06:10: 10000000 INFO @ Sat, 03 Apr 2021 07:06:11: 5000000 INFO @ Sat, 03 Apr 2021 07:06:15: 18000000 INFO @ Sat, 03 Apr 2021 07:06:17: 11000000 INFO @ Sat, 03 Apr 2021 07:06:17: 6000000 INFO @ Sat, 03 Apr 2021 07:06:20: 19000000 INFO @ Sat, 03 Apr 2021 07:06:23: 12000000 INFO @ Sat, 03 Apr 2021 07:06:23: 7000000 INFO @ Sat, 03 Apr 2021 07:06:26: 20000000 INFO @ Sat, 03 Apr 2021 07:06:29: 13000000 INFO @ Sat, 03 Apr 2021 07:06:30: 8000000 INFO @ Sat, 03 Apr 2021 07:06:31: 21000000 INFO @ Sat, 03 Apr 2021 07:06:35: 14000000 INFO @ Sat, 03 Apr 2021 07:06:36: 9000000 INFO @ Sat, 03 Apr 2021 07:06:37: 22000000 INFO @ Sat, 03 Apr 2021 07:06:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:06:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:06:37: #1 total tags in treatment: 9152290 INFO @ Sat, 03 Apr 2021 07:06:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:06:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:06:37: #1 tags after filtering in treatment: 7559197 INFO @ Sat, 03 Apr 2021 07:06:37: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 07:06:37: #1 finished! INFO @ Sat, 03 Apr 2021 07:06:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:06:38: #2 number of paired peaks: 228 WARNING @ Sat, 03 Apr 2021 07:06:38: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sat, 03 Apr 2021 07:06:38: start model_add_line... INFO @ Sat, 03 Apr 2021 07:06:38: start X-correlation... INFO @ Sat, 03 Apr 2021 07:06:38: end of X-cor INFO @ Sat, 03 Apr 2021 07:06:38: #2 finished! INFO @ Sat, 03 Apr 2021 07:06:38: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 07:06:38: #2 alternative fragment length(s) may be 4,68,94,573 bps INFO @ Sat, 03 Apr 2021 07:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.05_model.r WARNING @ Sat, 03 Apr 2021 07:06:38: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:06:38: #2 You may need to consider one of the other alternative d(s): 4,68,94,573 WARNING @ Sat, 03 Apr 2021 07:06:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:06:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:06:41: 15000000 INFO @ Sat, 03 Apr 2021 07:06:42: 10000000 INFO @ Sat, 03 Apr 2021 07:06:47: 16000000 INFO @ Sat, 03 Apr 2021 07:06:49: 11000000 INFO @ Sat, 03 Apr 2021 07:06:53: 17000000 INFO @ Sat, 03 Apr 2021 07:06:55: 12000000 INFO @ Sat, 03 Apr 2021 07:06:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:06:59: 18000000 INFO @ Sat, 03 Apr 2021 07:07:01: 13000000 INFO @ Sat, 03 Apr 2021 07:07:05: 19000000 INFO @ Sat, 03 Apr 2021 07:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.05_summits.bed INFO @ Sat, 03 Apr 2021 07:07:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3175 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:07:07: 14000000 INFO @ Sat, 03 Apr 2021 07:07:12: 20000000 INFO @ Sat, 03 Apr 2021 07:07:13: 15000000 INFO @ Sat, 03 Apr 2021 07:07:18: 21000000 INFO @ Sat, 03 Apr 2021 07:07:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:07:24: 22000000 INFO @ Sat, 03 Apr 2021 07:07:24: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:24: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:24: #1 total tags in treatment: 9152290 INFO @ Sat, 03 Apr 2021 07:07:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:25: #1 tags after filtering in treatment: 7559197 INFO @ Sat, 03 Apr 2021 07:07:25: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 07:07:25: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:25: #2 number of paired peaks: 228 WARNING @ Sat, 03 Apr 2021 07:07:25: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:25: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:25: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:25: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:25: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:25: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 07:07:25: #2 alternative fragment length(s) may be 4,68,94,573 bps INFO @ Sat, 03 Apr 2021 07:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.10_model.r WARNING @ Sat, 03 Apr 2021 07:07:25: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:25: #2 You may need to consider one of the other alternative d(s): 4,68,94,573 WARNING @ Sat, 03 Apr 2021 07:07:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:25: 17000000 INFO @ Sat, 03 Apr 2021 07:07:31: 18000000 INFO @ Sat, 03 Apr 2021 07:07:37: 19000000 INFO @ Sat, 03 Apr 2021 07:07:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:07:44: 20000000 INFO @ Sat, 03 Apr 2021 07:07:50: 21000000 INFO @ Sat, 03 Apr 2021 07:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.10_summits.bed INFO @ Sat, 03 Apr 2021 07:07:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:07:55: 22000000 INFO @ Sat, 03 Apr 2021 07:07:56: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:07:56: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:07:56: #1 total tags in treatment: 9152290 INFO @ Sat, 03 Apr 2021 07:07:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:07:56: #1 tags after filtering in treatment: 7559197 INFO @ Sat, 03 Apr 2021 07:07:56: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 07:07:56: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:57: #2 number of paired peaks: 228 WARNING @ Sat, 03 Apr 2021 07:07:57: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:57: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:57: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:57: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:57: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:57: #2 predicted fragment length is 94 bps INFO @ Sat, 03 Apr 2021 07:07:57: #2 alternative fragment length(s) may be 4,68,94,573 bps INFO @ Sat, 03 Apr 2021 07:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.20_model.r WARNING @ Sat, 03 Apr 2021 07:07:57: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:07:57: #2 You may need to consider one of the other alternative d(s): 4,68,94,573 WARNING @ Sat, 03 Apr 2021 07:07:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:07:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:08:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430373/SRX6430373.20_summits.bed INFO @ Sat, 03 Apr 2021 07:08:24: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling