[2023-07-01 07:47:36,170] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:47:36,200] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:47:36,201] [INFO] DQC Reference Directory: /var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference
[2023-07-01 07:47:39,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:47:39,673] [INFO] Task started: Prodigal
[2023-07-01 07:47:39,674] [INFO] Running command: gunzip -c /var/lib/cwl/stg5f462d41-230d-4fa7-84f7-0a37af7c9205/GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna.gz | prodigal -d GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/cds.fna -a GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:47:51,279] [INFO] Task succeeded: Prodigal
[2023-07-01 07:47:51,280] [INFO] Task started: HMMsearch
[2023-07-01 07:47:51,280] [INFO] Running command: hmmsearch --tblout GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference/reference_markers.hmm GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:47:51,585] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:47:51,586] [INFO] Found 6/6 markers.
[2023-07-01 07:47:51,619] [INFO] Query marker FASTA was written to GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/markers.fasta
[2023-07-01 07:47:51,619] [INFO] Task started: Blastn
[2023-07-01 07:47:51,619] [INFO] Running command: blastn -query GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference/reference_markers.fasta -out GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:47:52,328] [INFO] Task succeeded: Blastn
[2023-07-01 07:47:52,332] [INFO] Selected 22 target genomes.
[2023-07-01 07:47:52,332] [INFO] Target genome list was writen to GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/target_genomes.txt
[2023-07-01 07:47:52,333] [INFO] Task started: fastANI
[2023-07-01 07:47:52,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f462d41-230d-4fa7-84f7-0a37af7c9205/GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna.gz --refList GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/target_genomes.txt --output GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:48:08,434] [INFO] Task succeeded: fastANI
[2023-07-01 07:48:08,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:48:08,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:48:08,456] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:48:08,457] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 07:48:08,457] [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
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	78.3523	400	1143	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	78.3236	345	1143	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	78.2977	367	1143	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	78.2402	371	1143	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	78.145	378	1143	95	below_threshold
Fundidesulfovibrio putealis	strain=DSM 16056	GCA_000429325.1	270496	270496	type	True	77.867	346	1143	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	77.7296	385	1143	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.7247	261	1143	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	77.6876	257	1143	95	below_threshold
Desulfohalovibrio alkalitolerans	strain=DSM 16529	GCA_000422245.1	293256	293256	type	True	77.5322	287	1143	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	77.5315	277	1143	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.4739	318	1143	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	77.4328	339	1143	95	below_threshold
Desulfocurvibacter africanus subsp. africanus	strain=DSM 2603	GCA_000422545.1	1511600	873	type	True	77.393	254	1143	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	77.3606	278	1143	95	below_threshold
Chromobacterium amazonense	strain=DSM 26508	GCA_001855565.1	1382803	1382803	type	True	75.4792	51	1143	95	below_threshold
Chromobacterium sinusclupearum	strain=MWU13-2610	GCA_002902845.1	2077146	2077146	type	True	75.3763	60	1143	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	75.3447	79	1143	95	below_threshold
Chromobacterium subtsugae	strain=PRAA4-1	GCA_001676875.1	251747	251747	type	True	75.3321	86	1143	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 07:48:08,459] [INFO] DFAST Taxonomy check result was written to GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/tc_result.tsv
[2023-07-01 07:48:08,460] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:48:08,460] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:48:08,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference/checkm_data
[2023-07-01 07:48:08,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:48:08,506] [INFO] Task started: CheckM
[2023-07-01 07:48:08,506] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/checkm_input GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/checkm_result
[2023-07-01 07:48:45,151] [INFO] Task succeeded: CheckM
[2023-07-01 07:48:45,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 07:48:45,173] [INFO] ===== Completeness check finished =====
[2023-07-01 07:48:45,174] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:48:45,174] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/markers.fasta)
[2023-07-01 07:48:45,175] [INFO] Task started: Blastn
[2023-07-01 07:48:45,175] [INFO] Running command: blastn -query GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bf1c13-0c7b-4069-b9e1-e0dcf78032e4/dqc_reference/reference_markers_gtdb.fasta -out GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:48:46,217] [INFO] Task succeeded: Blastn
[2023-07-01 07:48:46,223] [INFO] Selected 8 target genomes.
[2023-07-01 07:48:46,223] [INFO] Target genome list was writen to GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:48:46,225] [INFO] Task started: fastANI
[2023-07-01 07:48:46,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f462d41-230d-4fa7-84f7-0a37af7c9205/GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna.gz --refList GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/target_genomes_gtdb.txt --output GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:48:53,090] [INFO] Task succeeded: fastANI
[2023-07-01 07:48:53,102] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 07:48:53,102] [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_903843965.1	s__Humidesulfovibrio sp903843965	99.9428	1107	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.96	99.89	0.96	0.94	12	conclusive
GCA_001799475.1	s__Humidesulfovibrio sp001799475	88.3929	723	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840405.1	s__Humidesulfovibrio sp002840405	88.0513	860	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018817515.1	s__Humidesulfovibrio sp018817515	87.7443	831	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018822105.1	s__Humidesulfovibrio sp018822105	86.4278	783	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016218665.1	s__Humidesulfovibrio sp016218665	83.4654	625	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188225.1	s__Humidesulfovibrio mexicanus	81.8341	649	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001871085.1	s__Humidesulfovibrio sp001871085	81.496	579	1143	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 07:48:53,104] [INFO] GTDB search result was written to GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/result_gtdb.tsv
[2023-07-01 07:48:53,105] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:48:53,124] [INFO] DFAST_QC result json was written to GCA_903855535.1_freshwater_MAG_---_AM-2014-D5_bin-366_genomic.fna/dqc_result.json
[2023-07-01 07:48:53,125] [INFO] DFAST_QC completed!
[2023-07-01 07:48:53,125] [INFO] Total running time: 0h1m17s