[2024-01-24 12:16:04,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:05,000] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:05,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference
[2024-01-24 12:16:06,206] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:06,207] [INFO] Task started: Prodigal
[2024-01-24 12:16:06,207] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ee4b3db-6773-4904-9352-c87cab1c2e92/GCF_025165815.1_ASM2516581v1_genomic.fna.gz | prodigal -d GCF_025165815.1_ASM2516581v1_genomic.fna/cds.fna -a GCF_025165815.1_ASM2516581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:29,282] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:29,283] [INFO] Task started: HMMsearch
[2024-01-24 12:16:29,283] [INFO] Running command: hmmsearch --tblout GCF_025165815.1_ASM2516581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference/reference_markers.hmm GCF_025165815.1_ASM2516581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:29,635] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:29,636] [INFO] Found 6/6 markers.
[2024-01-24 12:16:29,695] [INFO] Query marker FASTA was written to GCF_025165815.1_ASM2516581v1_genomic.fna/markers.fasta
[2024-01-24 12:16:29,696] [INFO] Task started: Blastn
[2024-01-24 12:16:29,696] [INFO] Running command: blastn -query GCF_025165815.1_ASM2516581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference/reference_markers.fasta -out GCF_025165815.1_ASM2516581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:31,110] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:31,113] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:31,114] [INFO] Target genome list was writen to GCF_025165815.1_ASM2516581v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:31,122] [INFO] Task started: fastANI
[2024-01-24 12:16:31,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee4b3db-6773-4904-9352-c87cab1c2e92/GCF_025165815.1_ASM2516581v1_genomic.fna.gz --refList GCF_025165815.1_ASM2516581v1_genomic.fna/target_genomes.txt --output GCF_025165815.1_ASM2516581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:17:07,259] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:07,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:17:07,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:17:07,275] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:17:07,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:17:07,275] [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
Actinophytocola xinjiangensis	strain=CGMCC 4.4663	GCA_001921215.1	485602	485602	type	True	83.3074	1614	2434	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	83.1456	1485	2434	95	below_threshold
Actinophytocola algeriensis	strain=DSM 46746	GCA_014874055.1	1768010	1768010	type	True	81.548	1533	2434	95	below_threshold
Actinophytocola algeriensis	strain=CECT 8960	GCA_014203735.1	1768010	1768010	type	True	81.4691	1546	2434	95	below_threshold
Actinophytocola oryzae	strain=DSM 45499	GCA_004364325.1	502181	502181	type	True	80.593	1373	2434	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	79.5202	922	2434	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	79.4139	982	2434	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	79.3248	901	2434	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	79.2616	941	2434	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	79.0894	980	2434	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.8244	961	2434	95	below_threshold
Saccharopolyspora hordei	strain=DSM 44065	GCA_013410345.1	1838	1838	type	True	78.3328	812	2434	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	78.3236	1042	2434	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.267	896	2434	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.2571	1068	2434	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	78.1557	942	2434	95	below_threshold
Saccharopolyspora flava	strain=DSM 44771	GCA_900116135.1	95161	95161	type	True	78.1223	825	2434	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.1191	887	2434	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	78.0165	998	2434	95	below_threshold
Saccharopolyspora shandongensis	strain=CGMCC 4.3530	GCA_900106995.1	418495	418495	type	True	77.9936	896	2434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:17:07,277] [INFO] DFAST Taxonomy check result was written to GCF_025165815.1_ASM2516581v1_genomic.fna/tc_result.tsv
[2024-01-24 12:17:07,278] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:17:07,278] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:17:07,278] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference/checkm_data
[2024-01-24 12:17:07,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:17:07,344] [INFO] Task started: CheckM
[2024-01-24 12:17:07,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025165815.1_ASM2516581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025165815.1_ASM2516581v1_genomic.fna/checkm_input GCF_025165815.1_ASM2516581v1_genomic.fna/checkm_result
[2024-01-24 12:18:36,814] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:36,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:18:36,842] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:36,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:36,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025165815.1_ASM2516581v1_genomic.fna/markers.fasta)
[2024-01-24 12:18:36,843] [INFO] Task started: Blastn
[2024-01-24 12:18:36,843] [INFO] Running command: blastn -query GCF_025165815.1_ASM2516581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5711c82e-f715-4ebd-9543-c451617b7a84/dqc_reference/reference_markers_gtdb.fasta -out GCF_025165815.1_ASM2516581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:38,962] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:38,966] [INFO] Selected 18 target genomes.
[2024-01-24 12:18:38,966] [INFO] Target genome list was writen to GCF_025165815.1_ASM2516581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:38,998] [INFO] Task started: fastANI
[2024-01-24 12:18:38,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ee4b3db-6773-4904-9352-c87cab1c2e92/GCF_025165815.1_ASM2516581v1_genomic.fna.gz --refList GCF_025165815.1_ASM2516581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025165815.1_ASM2516581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:19:10,221] [INFO] Task succeeded: fastANI
[2024-01-24 12:19:10,237] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:19:10,238] [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_001921215.1	s__Actinophytocola xinjiangensis	83.2899	1618	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	83.2232	1472	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009379765.1	s__Actinophytocola sp009379765	82.8951	1384	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203735.1	s__Actinophytocola algeriensis	81.4965	1540	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364325.1	s__Actinophytocola oryzae	80.5984	1372	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	79.5205	922	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009745975.1	s__Actinokineospora pegani	79.3518	924	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216555.1	s__Herbihabitans rhizosphaerae	79.3303	964	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Herbihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900070365.1	s__Actinokineospora sp900070365	79.1805	935	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	79.1268	972	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	79.0865	1012	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362825.1	s__Labedaea rhizosphaerae	79.0462	1052	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011758765.1	s__Amycolatopsis viridis	78.6921	861	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.9842	N/A	N/A	N/A	N/A	1	-
GCF_008386585.1	s__AN110305 sp008386585	78.5287	1023	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__AN110305	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023245.1	s__Actinosynnema mirum	78.3379	1037	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	99.51	99.51	0.95	0.95	3	-
GCF_002354875.1	s__Actinosynnema auranticum	78.2248	1029	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	96.4703	100.00	100.00	1.00	1.00	2	-
GCF_017876405.1	s__Kibdelosporangium banguiense	78.1666	938	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116135.1	s__Saccharopolyspora flava	78.1351	824	2434	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:19:10,239] [INFO] GTDB search result was written to GCF_025165815.1_ASM2516581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:19:10,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:19:10,244] [INFO] DFAST_QC result json was written to GCF_025165815.1_ASM2516581v1_genomic.fna/dqc_result.json
[2024-01-24 12:19:10,244] [INFO] DFAST_QC completed!
[2024-01-24 12:19:10,244] [INFO] Total running time: 0h3m5s