[2023-06-28 12:03:46,369] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:03:46,375] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:03:46,376] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference
[2023-06-28 12:03:47,706] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:03:47,706] [INFO] Task started: Prodigal
[2023-06-28 12:03:47,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg68317eab-41b7-4b4e-80d0-b03398ec866c/GCA_944324585.1_E41_bin210_genomic.fna.gz | prodigal -d GCA_944324585.1_E41_bin210_genomic.fna/cds.fna -a GCA_944324585.1_E41_bin210_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:03:54,042] [INFO] Task succeeded: Prodigal
[2023-06-28 12:03:54,042] [INFO] Task started: HMMsearch
[2023-06-28 12:03:54,043] [INFO] Running command: hmmsearch --tblout GCA_944324585.1_E41_bin210_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference/reference_markers.hmm GCA_944324585.1_E41_bin210_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:03:54,264] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:03:54,265] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg68317eab-41b7-4b4e-80d0-b03398ec866c/GCA_944324585.1_E41_bin210_genomic.fna.gz]
[2023-06-28 12:03:54,290] [INFO] Query marker FASTA was written to GCA_944324585.1_E41_bin210_genomic.fna/markers.fasta
[2023-06-28 12:03:54,291] [INFO] Task started: Blastn
[2023-06-28 12:03:54,291] [INFO] Running command: blastn -query GCA_944324585.1_E41_bin210_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference/reference_markers.fasta -out GCA_944324585.1_E41_bin210_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:03:54,969] [INFO] Task succeeded: Blastn
[2023-06-28 12:03:54,974] [INFO] Selected 10 target genomes.
[2023-06-28 12:03:54,975] [INFO] Target genome list was writen to GCA_944324585.1_E41_bin210_genomic.fna/target_genomes.txt
[2023-06-28 12:03:54,976] [INFO] Task started: fastANI
[2023-06-28 12:03:54,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg68317eab-41b7-4b4e-80d0-b03398ec866c/GCA_944324585.1_E41_bin210_genomic.fna.gz --refList GCA_944324585.1_E41_bin210_genomic.fna/target_genomes.txt --output GCA_944324585.1_E41_bin210_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:04:01,884] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:01,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:04:01,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:04:01,895] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:04:01,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 12:04:01,895] [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
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	79.0199	287	676	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	78.5549	278	676	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	77.7382	186	676	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	77.144	123	676	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	76.8063	115	676	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	76.7358	112	676	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	76.7188	146	676	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.5076	81	676	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.9146	69	676	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	75.7525	77	676	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 12:04:01,897] [INFO] DFAST Taxonomy check result was written to GCA_944324585.1_E41_bin210_genomic.fna/tc_result.tsv
[2023-06-28 12:04:01,898] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:04:01,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:04:01,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference/checkm_data
[2023-06-28 12:04:01,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:04:01,932] [INFO] Task started: CheckM
[2023-06-28 12:04:01,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324585.1_E41_bin210_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324585.1_E41_bin210_genomic.fna/checkm_input GCA_944324585.1_E41_bin210_genomic.fna/checkm_result
[2023-06-28 12:04:26,337] [INFO] Task succeeded: CheckM
[2023-06-28 12:04:26,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 12:04:26,371] [INFO] ===== Completeness check finished =====
[2023-06-28 12:04:26,372] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:04:26,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324585.1_E41_bin210_genomic.fna/markers.fasta)
[2023-06-28 12:04:26,373] [INFO] Task started: Blastn
[2023-06-28 12:04:26,373] [INFO] Running command: blastn -query GCA_944324585.1_E41_bin210_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cf6600a-3c0b-4726-95ae-0348f1538ed8/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324585.1_E41_bin210_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:27,382] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:27,390] [INFO] Selected 11 target genomes.
[2023-06-28 12:04:27,391] [INFO] Target genome list was writen to GCA_944324585.1_E41_bin210_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:04:27,392] [INFO] Task started: fastANI
[2023-06-28 12:04:27,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg68317eab-41b7-4b4e-80d0-b03398ec866c/GCA_944324585.1_E41_bin210_genomic.fna.gz --refList GCA_944324585.1_E41_bin210_genomic.fna/target_genomes_gtdb.txt --output GCA_944324585.1_E41_bin210_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:04:35,447] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:35,462] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:04:35,462] [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
GCA_905215675.1	s__Desulfovibrio sp905215675	98.1794	477	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019114565.1	s__Desulfovibrio intestinigallinarum	86.6071	497	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116045.1	s__Desulfovibrio piger_A	79.3481	291	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCA_019118345.1	s__Desulfovibrio intestinavium	79.2281	285	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118745.1	s__Desulfovibrio gallistercoris	79.0991	299	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156375.1	s__Desulfovibrio piger	79.0037	288	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCF_012843875.1	s__Desulfovibrio sp900556755	78.9049	273	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	78.4931	247	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011039085.1	s__Desulfovibrio sp011039085	77.6215	216	676	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.72	96.72	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-28 12:04:35,465] [INFO] GTDB search result was written to GCA_944324585.1_E41_bin210_genomic.fna/result_gtdb.tsv
[2023-06-28 12:04:35,465] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:04:35,470] [INFO] DFAST_QC result json was written to GCA_944324585.1_E41_bin210_genomic.fna/dqc_result.json
[2023-06-28 12:04:35,470] [INFO] DFAST_QC completed!
[2023-06-28 12:04:35,470] [INFO] Total running time: 0h0m49s