[2024-01-24 11:12:58,139] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,141] [INFO] DQC Reference Directory: /var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference
[2024-01-24 11:12:59,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,536] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,536] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb7010c2-d974-4ec2-b90d-51affb9a2c24/GCF_014773365.1_ASM1477336v1_genomic.fna.gz | prodigal -d GCF_014773365.1_ASM1477336v1_genomic.fna/cds.fna -a GCF_014773365.1_ASM1477336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:08,031] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:08,031] [INFO] Task started: HMMsearch
[2024-01-24 11:13:08,031] [INFO] Running command: hmmsearch --tblout GCF_014773365.1_ASM1477336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference/reference_markers.hmm GCF_014773365.1_ASM1477336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:08,343] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:08,344] [INFO] Found 6/6 markers.
[2024-01-24 11:13:08,369] [INFO] Query marker FASTA was written to GCF_014773365.1_ASM1477336v1_genomic.fna/markers.fasta
[2024-01-24 11:13:08,369] [INFO] Task started: Blastn
[2024-01-24 11:13:08,370] [INFO] Running command: blastn -query GCF_014773365.1_ASM1477336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference/reference_markers.fasta -out GCF_014773365.1_ASM1477336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:09,043] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:09,046] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:09,046] [INFO] Target genome list was writen to GCF_014773365.1_ASM1477336v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:09,052] [INFO] Task started: fastANI
[2024-01-24 11:13:09,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb7010c2-d974-4ec2-b90d-51affb9a2c24/GCF_014773365.1_ASM1477336v1_genomic.fna.gz --refList GCF_014773365.1_ASM1477336v1_genomic.fna/target_genomes.txt --output GCF_014773365.1_ASM1477336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:19,569] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:19,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:19,570] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:19,579] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:19,579] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:19,579] [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
Pelovirga terrestris	strain=M08fum	GCA_014773365.1	2771352	2771352	type	True	100.0	1007	1009	95	conclusive
Geopsychrobacter electrodiphilus	strain=DSM 16401	GCA_000384395.1	225196	225196	type	True	77.1563	75	1009	95	below_threshold
Syntrophotalea acetylenica	strain=DSM 3246	GCA_001888165.1	29542	29542	type	True	77.1498	56	1009	95	below_threshold
Pelobacter seleniigenes	strain=DSM 18267	GCA_000711225.1	407188	407188	type	True	77.0894	135	1009	95	below_threshold
Malonomonas rubra	strain=DSM 5091	GCA_900142125.1	57040	57040	type	True	76.6668	104	1009	95	below_threshold
Geothermobacter ehrlichii	strain=SS015	GCA_008124615.1	213224	213224	type	True	76.663	70	1009	95	below_threshold
Desulfuromonas acetexigens		GCA_900111775.1	38815	38815	type	True	76.5018	66	1009	95	below_threshold
Desulfuromonas acetexigens	strain=2873	GCA_007051125.1	38815	38815	type	True	76.5018	66	1009	95	below_threshold
Desulfuromonas thiophila	strain=DSM 8987	GCA_900101955.1	57664	57664	type	True	76.473	52	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:19,581] [INFO] DFAST Taxonomy check result was written to GCF_014773365.1_ASM1477336v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:19,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:19,582] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:19,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference/checkm_data
[2024-01-24 11:13:19,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:19,615] [INFO] Task started: CheckM
[2024-01-24 11:13:19,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014773365.1_ASM1477336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014773365.1_ASM1477336v1_genomic.fna/checkm_input GCF_014773365.1_ASM1477336v1_genomic.fna/checkm_result
[2024-01-24 11:13:50,440] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:50,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:50,465] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:50,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:50,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014773365.1_ASM1477336v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:50,466] [INFO] Task started: Blastn
[2024-01-24 11:13:50,466] [INFO] Running command: blastn -query GCF_014773365.1_ASM1477336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02b2daa5-eca1-408e-b33e-c3ef198d94a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014773365.1_ASM1477336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:51,303] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:51,306] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:51,306] [INFO] Target genome list was writen to GCF_014773365.1_ASM1477336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:51,342] [INFO] Task started: fastANI
[2024-01-24 11:13:51,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb7010c2-d974-4ec2-b90d-51affb9a2c24/GCF_014773365.1_ASM1477336v1_genomic.fna.gz --refList GCF_014773365.1_ASM1477336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014773365.1_ASM1477336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:00,180] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:00,193] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:00,194] [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_014773365.1	s__Pelovirga terrestris	100.0	1007	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Pelovirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018399135.1	s__Pelovirga sp018399135	82.1054	597	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Pelovirga	95.0	99.36	99.36	0.85	0.85	2	-
GCA_007125165.1	s__Pelovirga sp007125165	79.7205	404	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Pelovirga	95.0	99.68	99.64	0.90	0.89	3	-
GCF_000711225.1	s__Seleniibacterium seleniigenes	77.0901	136	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Seleniibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003247215.1	s__Malonomonas rubra_A	77.0835	71	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869665.1	s__BM522 sp002869665	76.8077	96	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__BM522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142125.1	s__Malonomonas rubra	76.6668	104	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152145.1	s__Malonomonas sp013152145	76.5964	108	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111775.1	s__Trichloromonas acetexigens	76.5018	66	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Trichloromonadaceae;g__Trichloromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013138655.1	s__Malonomonas sp013138655	76.4314	78	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__Malonomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931615.1	s__BM522 sp016931615	76.4004	110	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__BM522	95.0	99.98	99.98	0.91	0.91	2	-
GCA_002868865.1	s__BM509 sp002868865	76.0813	80	1009	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Desulfuromonadales;f__Geopsychrobacteraceae;g__BM509	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:00,195] [INFO] GTDB search result was written to GCF_014773365.1_ASM1477336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:00,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:00,199] [INFO] DFAST_QC result json was written to GCF_014773365.1_ASM1477336v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:00,199] [INFO] DFAST_QC completed!
[2024-01-24 11:14:00,199] [INFO] Total running time: 0h1m2s