[2024-01-25 18:40:05,558] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,559] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference
[2024-01-25 18:40:06,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,664] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,665] [INFO] Running command: gunzip -c /var/lib/cwl/stge1619184-67e4-4cce-96d0-d3f730e51dad/GCF_024753205.1_ASM2475320v1_genomic.fna.gz | prodigal -d GCF_024753205.1_ASM2475320v1_genomic.fna/cds.fna -a GCF_024753205.1_ASM2475320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:22,601] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:22,601] [INFO] Task started: HMMsearch
[2024-01-25 18:40:22,601] [INFO] Running command: hmmsearch --tblout GCF_024753205.1_ASM2475320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference/reference_markers.hmm GCF_024753205.1_ASM2475320v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:22,861] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:22,862] [INFO] Found 6/6 markers.
[2024-01-25 18:40:22,904] [INFO] Query marker FASTA was written to GCF_024753205.1_ASM2475320v1_genomic.fna/markers.fasta
[2024-01-25 18:40:22,905] [INFO] Task started: Blastn
[2024-01-25 18:40:22,905] [INFO] Running command: blastn -query GCF_024753205.1_ASM2475320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference/reference_markers.fasta -out GCF_024753205.1_ASM2475320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:23,850] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:23,853] [INFO] Selected 10 target genomes.
[2024-01-25 18:40:23,853] [INFO] Target genome list was writen to GCF_024753205.1_ASM2475320v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:23,856] [INFO] Task started: fastANI
[2024-01-25 18:40:23,857] [INFO] Running command: fastANI --query /var/lib/cwl/stge1619184-67e4-4cce-96d0-d3f730e51dad/GCF_024753205.1_ASM2475320v1_genomic.fna.gz --refList GCF_024753205.1_ASM2475320v1_genomic.fna/target_genomes.txt --output GCF_024753205.1_ASM2475320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:37,627] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:37,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:37,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:37,635] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:37,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:37,635] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Massilia aurea	strain=JCM 13879	GCA_024753205.1	373040	373040	type	True	100.0	1792	1792	95	conclusive
Massilia timonae	strain=CCUG 45783	GCA_000315425.1	47229	47229	type	True	85.2692	1319	1792	95	below_threshold
Massilia arenae	strain=GEM5	GCA_008014745.1	2603288	2603288	type	True	85.1206	1295	1792	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	85.0275	1311	1792	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	83.2039	1091	1792	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	82.9703	1071	1792	95	below_threshold
Massilia aromaticivorans	strain=ML15P13	GCA_013003915.1	2725995	2725995	type	True	82.7484	1040	1792	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	82.3043	1075	1792	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	81.4833	950	1792	95	below_threshold
Massilia putida	strain=6NM-7	GCA_001941825.1	1141883	1141883	type	True	80.9946	953	1792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:37,636] [INFO] DFAST Taxonomy check result was written to GCF_024753205.1_ASM2475320v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:37,637] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:37,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:37,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference/checkm_data
[2024-01-25 18:40:37,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:37,691] [INFO] Task started: CheckM
[2024-01-25 18:40:37,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024753205.1_ASM2475320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024753205.1_ASM2475320v1_genomic.fna/checkm_input GCF_024753205.1_ASM2475320v1_genomic.fna/checkm_result
[2024-01-25 18:41:26,143] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:26,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:26,161] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:26,162] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:26,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024753205.1_ASM2475320v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:26,162] [INFO] Task started: Blastn
[2024-01-25 18:41:26,162] [INFO] Running command: blastn -query GCF_024753205.1_ASM2475320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fae58a4-2192-4330-a193-76ee3e695165/dqc_reference/reference_markers_gtdb.fasta -out GCF_024753205.1_ASM2475320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:28,045] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:28,048] [INFO] Selected 10 target genomes.
[2024-01-25 18:41:28,048] [INFO] Target genome list was writen to GCF_024753205.1_ASM2475320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:28,054] [INFO] Task started: fastANI
[2024-01-25 18:41:28,054] [INFO] Running command: fastANI --query /var/lib/cwl/stge1619184-67e4-4cce-96d0-d3f730e51dad/GCF_024753205.1_ASM2475320v1_genomic.fna.gz --refList GCF_024753205.1_ASM2475320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024753205.1_ASM2475320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:42,023] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:42,030] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:41:42,030] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014200505.1	s__Massilia aurea_B	94.9388	1549	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.34	95.34	0.91	0.91	2	-
GCA_014841595.1	s__Massilia sp014841595	94.172	1516	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	98.42	98.38	0.96	0.95	4	-
GCA_014841835.1	s__Massilia sp014841835	93.3834	1541	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315425.1	s__Massilia timonae	85.2774	1318	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	97.91	95.09	0.93	0.87	8	-
GCF_017582745.1	s__Massilia oculi	85.1054	1320	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.07	95.07	0.86	0.86	2	-
GCF_003719535.1	s__Massilia aurea_A	84.9804	1200	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	95.87	95.87	0.88	0.88	2	-
GCA_002339265.1	s__Massilia sp002339265	84.3649	1113	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	83.1796	1095	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112225.1	s__Massilia yuzhufengensis	82.9823	1069	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013003915.1	s__Massilia aromaticivorans	82.7388	1041	1792	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:42,032] [INFO] GTDB search result was written to GCF_024753205.1_ASM2475320v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:42,033] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:42,035] [INFO] DFAST_QC result json was written to GCF_024753205.1_ASM2475320v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:42,035] [INFO] DFAST_QC completed!
[2024-01-25 18:41:42,035] [INFO] Total running time: 0h1m36s