[2023-06-05 18:58:13,206] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:58:13,209] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:58:13,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference
[2023-06-05 18:58:14,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:58:14,383] [INFO] Task started: Prodigal
[2023-06-05 18:58:14,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfb5ec6f-9fec-421d-b53d-bd32941f77b0/GCA_934622005.1_ERR7738230_bin.166_genomic.fna.gz | prodigal -d GCA_934622005.1_ERR7738230_bin.166_genomic.fna/cds.fna -a GCA_934622005.1_ERR7738230_bin.166_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:58:24,059] [INFO] Task succeeded: Prodigal
[2023-06-05 18:58:24,060] [INFO] Task started: HMMsearch
[2023-06-05 18:58:24,060] [INFO] Running command: hmmsearch --tblout GCA_934622005.1_ERR7738230_bin.166_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference/reference_markers.hmm GCA_934622005.1_ERR7738230_bin.166_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:58:24,326] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:58:24,328] [INFO] Found 6/6 markers.
[2023-06-05 18:58:24,361] [INFO] Query marker FASTA was written to GCA_934622005.1_ERR7738230_bin.166_genomic.fna/markers.fasta
[2023-06-05 18:58:24,361] [INFO] Task started: Blastn
[2023-06-05 18:58:24,361] [INFO] Running command: blastn -query GCA_934622005.1_ERR7738230_bin.166_genomic.fna/markers.fasta -db /var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference/reference_markers.fasta -out GCA_934622005.1_ERR7738230_bin.166_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:25,029] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:25,033] [INFO] Selected 33 target genomes.
[2023-06-05 18:58:25,034] [INFO] Target genome list was writen to GCA_934622005.1_ERR7738230_bin.166_genomic.fna/target_genomes.txt
[2023-06-05 18:58:25,040] [INFO] Task started: fastANI
[2023-06-05 18:58:25,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb5ec6f-9fec-421d-b53d-bd32941f77b0/GCA_934622005.1_ERR7738230_bin.166_genomic.fna.gz --refList GCA_934622005.1_ERR7738230_bin.166_genomic.fna/target_genomes.txt --output GCA_934622005.1_ERR7738230_bin.166_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:58:52,830] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:52,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:58:52,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:58:52,844] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:58:52,844] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:58:52,844] [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
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	75.3172	68	1169	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	75.0967	80	1169	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.9072	117	1169	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.9031	91	1169	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.8905	94	1169	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8897	89	1169	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	74.8047	192	1169	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	74.7994	78	1169	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	74.7939	50	1169	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	74.7575	115	1169	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	74.7548	83	1169	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	74.7425	63	1169	95	below_threshold
Nocardia tenerifensis	strain=DSM 44704	GCA_003202065.1	228006	228006	type	True	74.7354	90	1169	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	74.717	57	1169	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	74.6644	58	1169	95	below_threshold
Nocardia takedensis	strain=NBRC 100417	GCA_000308695.1	259390	259390	type	True	74.6564	82	1169	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:58:52,846] [INFO] DFAST Taxonomy check result was written to GCA_934622005.1_ERR7738230_bin.166_genomic.fna/tc_result.tsv
[2023-06-05 18:58:52,847] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:58:52,847] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:58:52,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference/checkm_data
[2023-06-05 18:58:52,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:58:52,889] [INFO] Task started: CheckM
[2023-06-05 18:58:52,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934622005.1_ERR7738230_bin.166_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934622005.1_ERR7738230_bin.166_genomic.fna/checkm_input GCA_934622005.1_ERR7738230_bin.166_genomic.fna/checkm_result
[2023-06-05 18:59:25,830] [INFO] Task succeeded: CheckM
[2023-06-05 18:59:25,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:59:25,853] [INFO] ===== Completeness check finished =====
[2023-06-05 18:59:25,854] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:59:25,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934622005.1_ERR7738230_bin.166_genomic.fna/markers.fasta)
[2023-06-05 18:59:25,854] [INFO] Task started: Blastn
[2023-06-05 18:59:25,854] [INFO] Running command: blastn -query GCA_934622005.1_ERR7738230_bin.166_genomic.fna/markers.fasta -db /var/lib/cwl/stg8de05c72-1ca2-4258-a182-0428f889ffb6/dqc_reference/reference_markers_gtdb.fasta -out GCA_934622005.1_ERR7738230_bin.166_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:59:26,862] [INFO] Task succeeded: Blastn
[2023-06-05 18:59:26,867] [INFO] Selected 13 target genomes.
[2023-06-05 18:59:26,867] [INFO] Target genome list was writen to GCA_934622005.1_ERR7738230_bin.166_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:59:26,932] [INFO] Task started: fastANI
[2023-06-05 18:59:26,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb5ec6f-9fec-421d-b53d-bd32941f77b0/GCA_934622005.1_ERR7738230_bin.166_genomic.fna.gz --refList GCA_934622005.1_ERR7738230_bin.166_genomic.fna/target_genomes_gtdb.txt --output GCA_934622005.1_ERR7738230_bin.166_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:59:37,721] [INFO] Task succeeded: fastANI
[2023-06-05 18:59:37,743] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:59:37,744] [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_900547945.1	s__RUG572 sp900547945	97.9064	874	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	99.14	98.30	0.90	0.80	3	conclusive
GCA_900771305.1	s__RUG572 sp900771305	83.739	539	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016302985.1	s__RUG572 sp016302985	82.3955	489	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320225.1	s__RUG572 sp900320225	80.2063	495	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	99.22	98.67	0.91	0.88	3	-
GCA_017563185.1	s__RUG572 sp017563185	79.9505	334	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427485.1	s__RUG572 sp017427485	79.9381	492	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902803135.1	s__RUG572 sp902803135	79.8499	365	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761035.1	s__RUG572 sp902761035	79.6926	393	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769585.1	s__RUG572 sp902769585	79.5247	410	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017459225.1	s__RUG572 sp017459225	79.4986	284	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779075.1	s__RUG572 sp902779075	79.324	400	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017613085.1	s__RGIG8368 sp017613085	76.3032	101	1169	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RGIG8368	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:59:37,746] [INFO] GTDB search result was written to GCA_934622005.1_ERR7738230_bin.166_genomic.fna/result_gtdb.tsv
[2023-06-05 18:59:37,747] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:59:37,751] [INFO] DFAST_QC result json was written to GCA_934622005.1_ERR7738230_bin.166_genomic.fna/dqc_result.json
[2023-06-05 18:59:37,751] [INFO] DFAST_QC completed!
[2023-06-05 18:59:37,751] [INFO] Total running time: 0h1m25s