MuTect is giving empty result

Haiying7Haiying7 Heidelberg, GermanyMember

I ran MuTect on 2 samples, one tumor and one normal, and did not get any error message, but the result files are almost empty, only some titles there. Could any one please tell me what could be wrong?

Thank you very much.

The log file after running mutect:
[[email protected] temp]$ /usr/bin/java -Xmx4g -jar ${MuTect}mutect-1.1.7.jar --analysis_type MuTect --reference_sequence ${GATK_hg} --cosmic ${COSMIC} --dbsnp ${dbSNP} --intervals ${Intervals} --input_file:normal ../Lock/Picard/${Normal}.readgroups.bam --input_file:tumor ../Lock/Picard/${Tumor}.readgroups.bam --out ${Tumor}${Normal}_call_stats.out --coverage_file ${Tumor}${Normal}_coverage.wig.txt
INFO 14:14:10,849 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:14:10,853 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.1-0-g72492bb, Compiled 2015/01/21 17:10:56
INFO 14:14:10,856 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:14:10,862 HelpFormatter - For support and documentation go to
INFO 14:14:10,875 HelpFormatter - Program Args: --analysis_type MuTect --reference_sequence /home/kong/Haiying/Reference/GATK/Genome/human_g1k_v37.fasta --cosmic /home/kong/Haiying/Reference/MuTect/COSMIC/b37_cosmic_v54_120711.vcf --dbsnp /home/kong/Haiying/Reference/MuTect/dbSNP/dbsnp_132_b37.leftAligned.vcf --intervals /home/kong/Haiying/Reference/Agilent/S04380219.bed --input_file:normal ../Lock/Picard/83115_ATCACG_L001.readgroups.bam --input_file:tumor ../Lock/Picard/2378_CTTGTA_L006.readgroups.bam --out 2378_CTTGTA_L006_83115_ATCACG_L001_call_stats.out --coverage_file 2378_CTTGTA_L006_83115_ATCACG_L001_coverage.wig.txt
INFO 14:14:10,890 HelpFormatter - Executing as [email protected] on Linux 2.6.18-371.9.1.el5 amd64; OpenJDK 64-Bit Server VM 1.7.0_79-mockbuild_2015_04_14_19_36-b00.
INFO 14:14:10,890 HelpFormatter - Date/Time: 2015/10/14 14:14:10
INFO 14:14:10,891 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:14:10,891 HelpFormatter - --------------------------------------------------------------------------------
INFO 14:14:11,009 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:14:11,140 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 14:14:11,154 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 14:14:11,231 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.08
WARN 14:14:12,820 IntervalUtils - The interval file /home/kong/Haiying/Reference/Agilent/S04380219.bed contains no intervals that could be parsed.
INFO 14:14:12,823 IntervalUtils - Processing 0 bp from intervals
WARN 14:14:12,824 GenomeAnalysisEngine - The given combination of -L and -XL options results in an empty set. No intervals to process.
INFO 14:14:12,928 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
INFO 14:14:12,932 GenomeAnalysisEngine - Done preparing for traversal
INFO 14:14:12,933 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining
INFO 14:14:12,935 MuTect - VERSION INFO: MuTect:1.1.6-4-g69b7a37 Gatk:3.1-0-g72492bb
INFO 14:14:12,951 Walker - [REDUCE RESULT] Traversal result is: 0
INFO 14:14:12,962 ProgressMeter - done 0.00e+00 0.0 s 8.0 h 0.0% 0.0 s 0.0 s
INFO 14:14:12,964 ProgressMeter - Total runtime 0.03 secs, 0.00 min, 0.00 hours

And the two result files:

[[email protected] temp]$ more 2378_CTTGTA_L006_83115_ATCACG_L001_call_stats.out

MuTect:1.1.6-4-g69b7a37 Gatk:3.1-0-g72492bb

contig position context ref_allele alt_allele tumor_name normal_name score dbsnp_site covered power tumor_power normal_power normal_power_nsp normal_power_wsp total_reads map_Q
0_reads init_t_lod t_lod_fstar t_lod_fstar_forward t_lod_fstar_reverse tumor_f contaminant_fraction contaminant_lod t_q20_count t_ref_count t_alt_count t_ref_sum t_alt_sum t_ref_max_mapq t_alt
_max_mapq t_ins_count t_del_count normal_best_gt init_n_lod normal_f n_q20_count n_ref_count n_alt_count n_ref_sum n_alt_sum power_to_detect_positive_strand_artifact power_to_dete
ct_negative_strand_artifact strand_bias_counts tumor_alt_fpir_median tumor_alt_fpir_mad tumor_alt_rpir_median tumor_alt_rpir_mad observed_in_normals_count failure_reasons judgement

[[email protected] temp]$ more 2378_CTTGTA_L006_83115_ATCACG_L001_coverage.wig.txt
track type=wiggle_0 name=SomaticCoverage


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