[2024-01-24 14:05:01,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:01,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:01,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference
[2024-01-24 14:05:02,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:02,251] [INFO] Task started: Prodigal
[2024-01-24 14:05:02,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d668e75-94f6-4f36-a428-5545d0062ed5/GCF_019599465.1_ASM1959946v1_genomic.fna.gz | prodigal -d GCF_019599465.1_ASM1959946v1_genomic.fna/cds.fna -a GCF_019599465.1_ASM1959946v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:25,207] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:25,208] [INFO] Task started: HMMsearch
[2024-01-24 14:05:25,208] [INFO] Running command: hmmsearch --tblout GCF_019599465.1_ASM1959946v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference/reference_markers.hmm GCF_019599465.1_ASM1959946v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:25,424] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:25,425] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7d668e75-94f6-4f36-a428-5545d0062ed5/GCF_019599465.1_ASM1959946v1_genomic.fna.gz]
[2024-01-24 14:05:25,464] [INFO] Query marker FASTA was written to GCF_019599465.1_ASM1959946v1_genomic.fna/markers.fasta
[2024-01-24 14:05:25,464] [INFO] Task started: Blastn
[2024-01-24 14:05:25,464] [INFO] Running command: blastn -query GCF_019599465.1_ASM1959946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference/reference_markers.fasta -out GCF_019599465.1_ASM1959946v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:25,983] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:25,986] [INFO] Selected 7 target genomes.
[2024-01-24 14:05:25,986] [INFO] Target genome list was writen to GCF_019599465.1_ASM1959946v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:25,988] [INFO] Task started: fastANI
[2024-01-24 14:05:25,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d668e75-94f6-4f36-a428-5545d0062ed5/GCF_019599465.1_ASM1959946v1_genomic.fna.gz --refList GCF_019599465.1_ASM1959946v1_genomic.fna/target_genomes.txt --output GCF_019599465.1_ASM1959946v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:33,420] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:33,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:33,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:33,431] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:33,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:33,431] [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
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	100.0	1533	1537	95	conclusive
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	89.8193	1016	1537	95	below_threshold
Halomicroarcula pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	89.8016	1015	1537	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	84.0599	900	1537	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	83.9761	867	1537	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	82.3477	731	1537	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	82.3456	730	1537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:33,433] [INFO] DFAST Taxonomy check result was written to GCF_019599465.1_ASM1959946v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:33,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:33,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:33,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference/checkm_data
[2024-01-24 14:05:33,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:33,491] [INFO] Task started: CheckM
[2024-01-24 14:05:33,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019599465.1_ASM1959946v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019599465.1_ASM1959946v1_genomic.fna/checkm_input GCF_019599465.1_ASM1959946v1_genomic.fna/checkm_result
[2024-01-24 14:06:37,580] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:37,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:37,599] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:37,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:37,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019599465.1_ASM1959946v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:37,600] [INFO] Task started: Blastn
[2024-01-24 14:06:37,601] [INFO] Running command: blastn -query GCF_019599465.1_ASM1959946v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7be21c8-f99b-403d-a4fe-d572caf10681/dqc_reference/reference_markers_gtdb.fasta -out GCF_019599465.1_ASM1959946v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:38,098] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:38,101] [INFO] Selected 8 target genomes.
[2024-01-24 14:06:38,101] [INFO] Target genome list was writen to GCF_019599465.1_ASM1959946v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:38,108] [INFO] Task started: fastANI
[2024-01-24 14:06:38,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d668e75-94f6-4f36-a428-5545d0062ed5/GCF_019599465.1_ASM1959946v1_genomic.fna.gz --refList GCF_019599465.1_ASM1959946v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019599465.1_ASM1959946v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:46,570] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:46,578] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:06:46,578] [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_014647235.1	s__Halomicroarcula pellucida	89.8276	1015	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_010119205.1	s__Halomicroarcula limicola	83.973	867	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004681185.1	s__Halomicroarcula amylolytica	83.3327	863	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119195.1	s__Haloarcula salina	82.3638	728	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005406125.1	s__Haloarcula sp005406125	81.6225	733	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844335.1	s__Haloarcula taiwanensis	81.1994	650	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCF_008729015.1	s__Haloarcula sp008729015	81.1412	674	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000336895.1	s__Haloarcula argentinensis	80.7995	625	1537	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:46,580] [INFO] GTDB search result was written to GCF_019599465.1_ASM1959946v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:46,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:46,584] [INFO] DFAST_QC result json was written to GCF_019599465.1_ASM1959946v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:46,584] [INFO] DFAST_QC completed!
[2024-01-24 14:06:46,584] [INFO] Total running time: 0h1m46s