Job ID = 14171304 SRX = SRX9005667 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 726650 READS because READLEN < 1 Read 8198273 spots for SRR12515068/SRR12515068.sra Written 8198273 spots for SRR12515068/SRR12515068.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171852 ("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] 3 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 1 unmatched pairs [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] 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] 17 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1105814 / 6604651 = 0.1674 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 11:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.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 11:41:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:41:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:35: 1000000 INFO @ Sat, 11 Dec 2021 11:41:46: 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 11:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.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 11:41:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:41:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:56: 3000000 INFO @ Sat, 11 Dec 2021 11:42:06: 1000000 INFO @ Sat, 11 Dec 2021 11:42:07: 4000000 INFO @ Sat, 11 Dec 2021 11:42:16: 2000000 INFO @ Sat, 11 Dec 2021 11:42:18: 5000000 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 11:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.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 11:42:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:42:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:42:26: 3000000 INFO @ Sat, 11 Dec 2021 11:42:29: 6000000 INFO @ Sat, 11 Dec 2021 11:42:35: 1000000 INFO @ Sat, 11 Dec 2021 11:42:36: 4000000 INFO @ Sat, 11 Dec 2021 11:42:40: 7000000 INFO @ Sat, 11 Dec 2021 11:42:45: 2000000 INFO @ Sat, 11 Dec 2021 11:42:46: 5000000 INFO @ Sat, 11 Dec 2021 11:42:51: 8000000 INFO @ Sat, 11 Dec 2021 11:42:55: 3000000 INFO @ Sat, 11 Dec 2021 11:42:56: 6000000 INFO @ Sat, 11 Dec 2021 11:43:03: 9000000 INFO @ Sat, 11 Dec 2021 11:43:05: 4000000 INFO @ Sat, 11 Dec 2021 11:43:06: 7000000 INFO @ Sat, 11 Dec 2021 11:43:15: 5000000 INFO @ Sat, 11 Dec 2021 11:43:15: 10000000 INFO @ Sat, 11 Dec 2021 11:43:15: 8000000 INFO @ Sat, 11 Dec 2021 11:43:25: 6000000 INFO @ Sat, 11 Dec 2021 11:43:25: 9000000 INFO @ Sat, 11 Dec 2021 11:43:26: 11000000 INFO @ Sat, 11 Dec 2021 11:43:35: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:43:35: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:43:35: #1 total tags in treatment: 5399116 INFO @ Sat, 11 Dec 2021 11:43:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:35: #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 11:43:35: #1 tags after filtering in treatment: 4861063 INFO @ Sat, 11 Dec 2021 11:43:35: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:43:35: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:35: 7000000 INFO @ Sat, 11 Dec 2021 11:43:35: #2 number of paired peaks: 6148 INFO @ Sat, 11 Dec 2021 11:43:35: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:36: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:36: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:36: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:36: #2 predicted fragment length is 223 bps INFO @ Sat, 11 Dec 2021 11:43:36: #2 alternative fragment length(s) may be 223 bps INFO @ Sat, 11 Dec 2021 11:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.05_model.r INFO @ Sat, 11 Dec 2021 11:43:36: 10000000 WARNING @ Sat, 11 Dec 2021 11:43:36: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:43:36: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Sat, 11 Dec 2021 11:43:36: #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 11:43:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:45: 8000000 INFO @ Sat, 11 Dec 2021 11:43:46: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:43:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:54: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:43:54: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:43:54: #1 total tags in treatment: 5399116 INFO @ Sat, 11 Dec 2021 11:43:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:54: #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 11:43:54: #1 tags after filtering in treatment: 4861063 INFO @ Sat, 11 Dec 2021 11:43:54: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:43:54: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:55: #2 number of paired peaks: 6148 INFO @ Sat, 11 Dec 2021 11:43:55: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:55: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:55: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:55: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:55: #2 predicted fragment length is 223 bps INFO @ Sat, 11 Dec 2021 11:43:55: #2 alternative fragment length(s) may be 223 bps INFO @ Sat, 11 Dec 2021 11:43:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.10_model.r WARNING @ Sat, 11 Dec 2021 11:43:55: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:43:55: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Sat, 11 Dec 2021 11:43:55: #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 11:43:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:55: 9000000 INFO @ Sat, 11 Dec 2021 11:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.05_summits.bed INFO @ Sat, 11 Dec 2021 11:44:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7050 records, 4 fields): 114 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:44:05: 10000000 INFO @ Sat, 11 Dec 2021 11:44:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:44:15: 11000000 INFO @ Sat, 11 Dec 2021 11:44:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.10_summits.bed INFO @ Sat, 11 Dec 2021 11:44:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4905 records, 4 fields): 199 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:44:23: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:44:23: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:44:23: #1 total tags in treatment: 5399116 INFO @ Sat, 11 Dec 2021 11:44:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:44:23: #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 11:44:23: #1 tags after filtering in treatment: 4861063 INFO @ Sat, 11 Dec 2021 11:44:23: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 11:44:23: #1 finished! INFO @ Sat, 11 Dec 2021 11:44:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:44:24: #2 number of paired peaks: 6148 INFO @ Sat, 11 Dec 2021 11:44:24: start model_add_line... INFO @ Sat, 11 Dec 2021 11:44:24: start X-correlation... INFO @ Sat, 11 Dec 2021 11:44:24: end of X-cor INFO @ Sat, 11 Dec 2021 11:44:24: #2 finished! INFO @ Sat, 11 Dec 2021 11:44:24: #2 predicted fragment length is 223 bps INFO @ Sat, 11 Dec 2021 11:44:24: #2 alternative fragment length(s) may be 223 bps INFO @ Sat, 11 Dec 2021 11:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.20_model.r WARNING @ Sat, 11 Dec 2021 11:44:24: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:44:24: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Sat, 11 Dec 2021 11:44:24: #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 11:44:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:44:24: #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 11:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005667/SRX9005667.20_summits.bed INFO @ Sat, 11 Dec 2021 11:44:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2938 records, 4 fields): 5 millis CompletedMACS2peakCalling