Job ID = 14171290 SRX = SRX9005660 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 797963 READS because READLEN < 1 Read 9277778 spots for SRR12515061/SRR12515061.sra Written 9277778 spots for SRR12515061/SRR12515061.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171841 ("srTdm6") has been submitted Time loading reference: 00:00:00 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] 1 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 2 unmatched pairs [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] 9 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1113987 / 7709575 = 0.1445 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.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, 11 Dec 2021 11:40:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:36: 1000000 INFO @ Sat, 11 Dec 2021 11:40:48: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.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, 11 Dec 2021 11:40:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:59: 3000000 INFO @ Sat, 11 Dec 2021 11:41:07: 1000000 INFO @ Sat, 11 Dec 2021 11:41:10: 4000000 INFO @ Sat, 11 Dec 2021 11:41:19: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:41:22: 5000000 INFO @ Sat, 11 Dec 2021 11:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.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, 11 Dec 2021 11:41:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:41:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:31: 3000000 INFO @ Sat, 11 Dec 2021 11:41:35: 6000000 INFO @ Sat, 11 Dec 2021 11:41:38: 1000000 INFO @ Sat, 11 Dec 2021 11:41:42: 4000000 INFO @ Sat, 11 Dec 2021 11:41:48: 7000000 INFO @ Sat, 11 Dec 2021 11:41:52: 2000000 INFO @ Sat, 11 Dec 2021 11:41:55: 5000000 INFO @ Sat, 11 Dec 2021 11:42:01: 8000000 INFO @ Sat, 11 Dec 2021 11:42:05: 3000000 INFO @ Sat, 11 Dec 2021 11:42:08: 6000000 INFO @ Sat, 11 Dec 2021 11:42:14: 9000000 INFO @ Sat, 11 Dec 2021 11:42:19: 4000000 INFO @ Sat, 11 Dec 2021 11:42:20: 7000000 INFO @ Sat, 11 Dec 2021 11:42:27: 10000000 INFO @ Sat, 11 Dec 2021 11:42:32: 5000000 INFO @ Sat, 11 Dec 2021 11:42:32: 8000000 INFO @ Sat, 11 Dec 2021 11:42:39: 11000000 INFO @ Sat, 11 Dec 2021 11:42:44: 9000000 INFO @ Sat, 11 Dec 2021 11:42:47: 6000000 INFO @ Sat, 11 Dec 2021 11:42:52: 12000000 INFO @ Sat, 11 Dec 2021 11:42:57: 10000000 INFO @ Sat, 11 Dec 2021 11:43:00: 7000000 INFO @ Sat, 11 Dec 2021 11:43:05: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:43:09: 11000000 INFO @ Sat, 11 Dec 2021 11:43:13: 8000000 INFO @ Sat, 11 Dec 2021 11:43:18: 14000000 INFO @ Sat, 11 Dec 2021 11:43:19: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:43:19: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:43:19: #1 total tags in treatment: 6485665 INFO @ Sat, 11 Dec 2021 11:43:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:43:19: #1 tags after filtering in treatment: 5831378 INFO @ Sat, 11 Dec 2021 11:43:19: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:43:19: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:20: #2 number of paired peaks: 5269 INFO @ Sat, 11 Dec 2021 11:43:20: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:20: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:20: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:20: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:20: #2 predicted fragment length is 222 bps INFO @ Sat, 11 Dec 2021 11:43:20: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 11 Dec 2021 11:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.05_model.r WARNING @ Sat, 11 Dec 2021 11:43:20: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:43:20: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Sat, 11 Dec 2021 11:43:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:43:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:22: 12000000 INFO @ Sat, 11 Dec 2021 11:43:25: 9000000 INFO @ Sat, 11 Dec 2021 11:43:34: 13000000 INFO @ Sat, 11 Dec 2021 11:43:36: 10000000 INFO @ Sat, 11 Dec 2021 11:43:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:43:46: 14000000 INFO @ Sat, 11 Dec 2021 11:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.05_summits.bed INFO @ Sat, 11 Dec 2021 11:43:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8407 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:43:47: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:43:47: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:43:47: #1 total tags in treatment: 6485665 INFO @ Sat, 11 Dec 2021 11:43:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:43:47: #1 tags after filtering in treatment: 5831378 INFO @ Sat, 11 Dec 2021 11:43:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:43:47: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:48: 11000000 INFO @ Sat, 11 Dec 2021 11:43:48: #2 number of paired peaks: 5269 INFO @ Sat, 11 Dec 2021 11:43:48: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:48: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:48: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:48: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:48: #2 predicted fragment length is 222 bps INFO @ Sat, 11 Dec 2021 11:43:48: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 11 Dec 2021 11:43:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.10_model.r WARNING @ Sat, 11 Dec 2021 11:43:48: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:43:48: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Sat, 11 Dec 2021 11:43:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:43:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:59: 12000000 INFO @ Sat, 11 Dec 2021 11:44:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:10: 13000000 INFO @ Sat, 11 Dec 2021 11:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.10_summits.bed INFO @ Sat, 11 Dec 2021 11:44:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6375 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:44:21: 14000000 INFO @ Sat, 11 Dec 2021 11:44:22: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:44:22: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:44:22: #1 total tags in treatment: 6485665 INFO @ Sat, 11 Dec 2021 11:44:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:44:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:44:22: #1 tags after filtering in treatment: 5831378 INFO @ Sat, 11 Dec 2021 11:44:22: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:44:22: #1 finished! INFO @ Sat, 11 Dec 2021 11:44:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:44:22: #2 number of paired peaks: 5269 INFO @ Sat, 11 Dec 2021 11:44:22: start model_add_line... INFO @ Sat, 11 Dec 2021 11:44:23: start X-correlation... INFO @ Sat, 11 Dec 2021 11:44:23: end of X-cor INFO @ Sat, 11 Dec 2021 11:44:23: #2 finished! INFO @ Sat, 11 Dec 2021 11:44:23: #2 predicted fragment length is 222 bps INFO @ Sat, 11 Dec 2021 11:44:23: #2 alternative fragment length(s) may be 222 bps INFO @ Sat, 11 Dec 2021 11:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.20_model.r WARNING @ Sat, 11 Dec 2021 11:44:23: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:44:23: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Sat, 11 Dec 2021 11:44:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:44:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:44:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:44:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005660/SRX9005660.20_summits.bed INFO @ Sat, 11 Dec 2021 11:44:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3945 records, 4 fields): 7 millis CompletedMACS2peakCalling