[2024-01-24 13:01:25,836] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:25,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:25,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference
[2024-01-24 13:01:27,321] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,322] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,323] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb3720fb-22bc-4dba-ae48-5f3908af31de/GCF_004345255.1_ASM434525v1_genomic.fna.gz | prodigal -d GCF_004345255.1_ASM434525v1_genomic.fna/cds.fna -a GCF_004345255.1_ASM434525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:38,550] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:38,550] [INFO] Task started: HMMsearch
[2024-01-24 13:01:38,550] [INFO] Running command: hmmsearch --tblout GCF_004345255.1_ASM434525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference/reference_markers.hmm GCF_004345255.1_ASM434525v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:38,904] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:38,905] [INFO] Found 6/6 markers.
[2024-01-24 13:01:38,945] [INFO] Query marker FASTA was written to GCF_004345255.1_ASM434525v1_genomic.fna/markers.fasta
[2024-01-24 13:01:38,945] [INFO] Task started: Blastn
[2024-01-24 13:01:38,945] [INFO] Running command: blastn -query GCF_004345255.1_ASM434525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference/reference_markers.fasta -out GCF_004345255.1_ASM434525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:39,586] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:39,590] [INFO] Selected 16 target genomes.
[2024-01-24 13:01:39,590] [INFO] Target genome list was writen to GCF_004345255.1_ASM434525v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:39,596] [INFO] Task started: fastANI
[2024-01-24 13:01:39,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb3720fb-22bc-4dba-ae48-5f3908af31de/GCF_004345255.1_ASM434525v1_genomic.fna.gz --refList GCF_004345255.1_ASM434525v1_genomic.fna/target_genomes.txt --output GCF_004345255.1_ASM434525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:52,726] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:52,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:52,727] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:52,734] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:52,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:52,735] [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
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	100.0	1520	1520	95	conclusive
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	99.9979	1520	1520	95	conclusive
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	77.4053	62	1520	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.9051	84	1520	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.7459	87	1520	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.291	109	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:52,736] [INFO] DFAST Taxonomy check result was written to GCF_004345255.1_ASM434525v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:52,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:52,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:52,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference/checkm_data
[2024-01-24 13:01:52,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:52,786] [INFO] Task started: CheckM
[2024-01-24 13:01:52,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345255.1_ASM434525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345255.1_ASM434525v1_genomic.fna/checkm_input GCF_004345255.1_ASM434525v1_genomic.fna/checkm_result
[2024-01-24 13:02:29,212] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:29,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:29,241] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:29,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:29,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345255.1_ASM434525v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:29,242] [INFO] Task started: Blastn
[2024-01-24 13:02:29,242] [INFO] Running command: blastn -query GCF_004345255.1_ASM434525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e2bd437-1fce-44b0-9cda-84238d35b9bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345255.1_ASM434525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:30,317] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:30,321] [INFO] Selected 23 target genomes.
[2024-01-24 13:02:30,322] [INFO] Target genome list was writen to GCF_004345255.1_ASM434525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:30,359] [INFO] Task started: fastANI
[2024-01-24 13:02:30,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb3720fb-22bc-4dba-ae48-5f3908af31de/GCF_004345255.1_ASM434525v1_genomic.fna.gz --refList GCF_004345255.1_ASM434525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345255.1_ASM434525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:44,402] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:44,430] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:44,430] [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_000732725.1	s__Kineothrix alysoides	99.9979	1520	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_012520655.1	s__Kineothrix sp012520655	80.4473	626	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403275.2	s__Kineothrix sp000403275	77.3374	180	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	98.66	98.53	0.88	0.87	4	-
GCA_011958945.1	s__Kineothrix sp011958945	77.3293	143	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	98.22	97.96	0.71	0.68	3	-
GCA_910588855.1	s__Kineothrix sp910588855	77.0938	167	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585965.1	s__Kineothrix sp910585965	76.9959	154	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520645.1	s__JAAYNV01 sp012520645	76.9673	98	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432425.1	s__CAG-510 sp002432425	76.8463	67	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	97.90	96.14	0.90	0.83	7	-
GCA_017624235.1	s__JAAYNV01 sp017624235	76.8236	81	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__JAAYNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434615.1	s__CAG-510 sp000434615	76.6587	72	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	98.10	97.86	0.88	0.86	6	-
GCA_910575245.1	s__UBA3282 sp910575245	76.6169	92	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.49	99.49	0.95	0.95	2	-
GCA_002492465.1	s__CAG-95 sp002492465	76.6044	74	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578115.1	s__UBA3282 sp910578115	76.5067	73	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588955.1	s__UBA3282 sp910588955	76.4993	60	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586025.1	s__CAG-95 sp910586025	76.4471	86	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804565.1	s__UBA3282 sp014804565	76.3898	59	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003488965.1	s__Kineothrix sp003488965	76.3649	89	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Kineothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774655.1	s__UBA3282 sp009774655	76.2342	68	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	98.36	98.36	0.78	0.78	2	-
GCA_910587715.1	s__UBA3282 sp910587715	76.0284	82	1520	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,432] [INFO] GTDB search result was written to GCF_004345255.1_ASM434525v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:44,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:44,436] [INFO] DFAST_QC result json was written to GCF_004345255.1_ASM434525v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:44,437] [INFO] DFAST_QC completed!
[2024-01-24 13:02:44,437] [INFO] Total running time: 0h1m19s