[2024-01-24 13:17:15,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference
[2024-01-24 13:17:16,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,918] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ff99eef-5e96-4b75-80b7-b1e0104e6311/GCF_019599515.1_ASM1959951v1_genomic.fna.gz | prodigal -d GCF_019599515.1_ASM1959951v1_genomic.fna/cds.fna -a GCF_019599515.1_ASM1959951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:37,724] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:37,725] [INFO] Task started: HMMsearch
[2024-01-24 13:17:37,725] [INFO] Running command: hmmsearch --tblout GCF_019599515.1_ASM1959951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference/reference_markers.hmm GCF_019599515.1_ASM1959951v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:38,009] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:38,011] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6ff99eef-5e96-4b75-80b7-b1e0104e6311/GCF_019599515.1_ASM1959951v1_genomic.fna.gz]
[2024-01-24 13:17:38,047] [INFO] Query marker FASTA was written to GCF_019599515.1_ASM1959951v1_genomic.fna/markers.fasta
[2024-01-24 13:17:38,048] [INFO] Task started: Blastn
[2024-01-24 13:17:38,048] [INFO] Running command: blastn -query GCF_019599515.1_ASM1959951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference/reference_markers.fasta -out GCF_019599515.1_ASM1959951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:38,619] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:38,623] [INFO] Selected 7 target genomes.
[2024-01-24 13:17:38,623] [INFO] Target genome list was writen to GCF_019599515.1_ASM1959951v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:38,627] [INFO] Task started: fastANI
[2024-01-24 13:17:38,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff99eef-5e96-4b75-80b7-b1e0104e6311/GCF_019599515.1_ASM1959951v1_genomic.fna.gz --refList GCF_019599515.1_ASM1959951v1_genomic.fna/target_genomes.txt --output GCF_019599515.1_ASM1959951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:46,649] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:46,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:46,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:46,661] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:46,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:46,662] [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 pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	100.0	1304	1304	95	conclusive
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	99.9937	1301	1304	95	conclusive
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	89.8899	1010	1304	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	83.727	842	1304	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	83.604	849	1304	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	81.9248	741	1304	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	81.9002	735	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,663] [INFO] DFAST Taxonomy check result was written to GCF_019599515.1_ASM1959951v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:46,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:46,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:46,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference/checkm_data
[2024-01-24 13:17:46,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:46,704] [INFO] Task started: CheckM
[2024-01-24 13:17:46,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019599515.1_ASM1959951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019599515.1_ASM1959951v1_genomic.fna/checkm_input GCF_019599515.1_ASM1959951v1_genomic.fna/checkm_result
[2024-01-24 13:18:40,427] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:40,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:40,451] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:40,452] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:40,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019599515.1_ASM1959951v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:40,453] [INFO] Task started: Blastn
[2024-01-24 13:18:40,453] [INFO] Running command: blastn -query GCF_019599515.1_ASM1959951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e338cb2-70eb-4595-bbbd-a55f9544d4db/dqc_reference/reference_markers_gtdb.fasta -out GCF_019599515.1_ASM1959951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:40,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:40,944] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:40,944] [INFO] Target genome list was writen to GCF_019599515.1_ASM1959951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:40,968] [INFO] Task started: fastANI
[2024-01-24 13:18:40,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ff99eef-5e96-4b75-80b7-b1e0104e6311/GCF_019599515.1_ASM1959951v1_genomic.fna.gz --refList GCF_019599515.1_ASM1959951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019599515.1_ASM1959951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:47,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:47,302] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:47,303] [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	99.9937	1301	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	conclusive
GCF_010119205.1	s__Halomicroarcula limicola	83.6383	846	1304	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	83.0511	871	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021755.1	s__Halomicroarcula sp003021755	81.9568	422	1304	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	81.9252	733	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002844335.1	s__Haloarcula taiwanensis	80.9577	666	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCF_014647415.1	s__Haloarcula sebkhae	80.4929	665	1304	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	95.97	95.97	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:47,304] [INFO] GTDB search result was written to GCF_019599515.1_ASM1959951v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:47,304] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:47,307] [INFO] DFAST_QC result json was written to GCF_019599515.1_ASM1959951v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:47,307] [INFO] DFAST_QC completed!
[2024-01-24 13:18:47,307] [INFO] Total running time: 0h1m32s