[2024-01-24 13:49:12,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:12,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:12,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference
[2024-01-24 13:49:14,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:14,295] [INFO] Task started: Prodigal
[2024-01-24 13:49:14,296] [INFO] Running command: gunzip -c /var/lib/cwl/stga16b0a09-80fb-4221-a2b3-b93d1d261ab2/GCF_003569045.1_Grel_assembly01_genomic.fna.gz | prodigal -d GCF_003569045.1_Grel_assembly01_genomic.fna/cds.fna -a GCF_003569045.1_Grel_assembly01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,058] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,058] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,059] [INFO] Running command: hmmsearch --tblout GCF_003569045.1_Grel_assembly01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference/reference_markers.hmm GCF_003569045.1_Grel_assembly01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,472] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,563] [INFO] Query marker FASTA was written to GCF_003569045.1_Grel_assembly01_genomic.fna/markers.fasta
[2024-01-24 13:49:34,563] [INFO] Task started: Blastn
[2024-01-24 13:49:34,564] [INFO] Running command: blastn -query GCF_003569045.1_Grel_assembly01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference/reference_markers.fasta -out GCF_003569045.1_Grel_assembly01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,358] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,361] [INFO] Selected 28 target genomes.
[2024-01-24 13:49:35,361] [INFO] Target genome list was writen to GCF_003569045.1_Grel_assembly01_genomic.fna/target_genomes.txt
[2024-01-24 13:49:35,378] [INFO] Task started: fastANI
[2024-01-24 13:49:35,379] [INFO] Running command: fastANI --query /var/lib/cwl/stga16b0a09-80fb-4221-a2b3-b93d1d261ab2/GCF_003569045.1_Grel_assembly01_genomic.fna.gz --refList GCF_003569045.1_Grel_assembly01_genomic.fna/target_genomes.txt --output GCF_003569045.1_Grel_assembly01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,695] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,696] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,715] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:58,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,715] [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
Aggregatilinea lenta	strain=MO-CFX2	GCA_003569045.1	913108	913108	type	True	100.0	2065	2065	95	conclusive
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.318	59	2065	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	74.9406	65	2065	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.8786	117	2065	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	74.8241	53	2065	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	74.7892	66	2065	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	74.7644	58	2065	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	74.7619	91	2065	95	below_threshold
Novosphingobium aerophilum	strain=4Y4	GCA_014230305.1	2839843	2839843	type	True	74.759	52	2065	95	below_threshold
Streptomyces fragilis	strain=NBRC 12862	GCA_003112515.1	67301	67301	type	True	74.7446	95	2065	95	below_threshold
Roseomonas harenae	strain=CPCC 101081	GCA_009848505.1	2692566	2692566	type	True	74.7412	67	2065	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	74.7324	52	2065	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	74.7294	99	2065	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.7259	135	2065	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	74.7112	95	2065	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	74.6657	109	2065	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	74.6462	135	2065	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	74.6319	101	2065	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	74.5703	52	2065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,718] [INFO] DFAST Taxonomy check result was written to GCF_003569045.1_Grel_assembly01_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,719] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference/checkm_data
[2024-01-24 13:49:58,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,798] [INFO] Task started: CheckM
[2024-01-24 13:49:58,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003569045.1_Grel_assembly01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003569045.1_Grel_assembly01_genomic.fna/checkm_input GCF_003569045.1_Grel_assembly01_genomic.fna/checkm_result
[2024-01-24 13:50:54,562] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:54,563] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:54,587] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:54,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:54,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003569045.1_Grel_assembly01_genomic.fna/markers.fasta)
[2024-01-24 13:50:54,589] [INFO] Task started: Blastn
[2024-01-24 13:50:54,589] [INFO] Running command: blastn -query GCF_003569045.1_Grel_assembly01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fff0588-b689-4acc-bdd2-0205705b7b31/dqc_reference/reference_markers_gtdb.fasta -out GCF_003569045.1_Grel_assembly01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:55,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:55,699] [INFO] Selected 12 target genomes.
[2024-01-24 13:50:55,699] [INFO] Target genome list was writen to GCF_003569045.1_Grel_assembly01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:55,734] [INFO] Task started: fastANI
[2024-01-24 13:50:55,734] [INFO] Running command: fastANI --query /var/lib/cwl/stga16b0a09-80fb-4221-a2b3-b93d1d261ab2/GCF_003569045.1_Grel_assembly01_genomic.fna.gz --refList GCF_003569045.1_Grel_assembly01_genomic.fna/target_genomes_gtdb.txt --output GCF_003569045.1_Grel_assembly01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:05,859] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:05,873] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:05,873] [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_003569045.1	s__Aggregatilinea lenta	100.0	2065	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__Aggregatilinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018432315.1	s__LM3-B42 sp018432315	78.4151	730	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__LM3-B42	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729765.1	s__JAAYCM01 sp012729765	78.3448	642	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JAAYCM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016926875.1	s__JAFGNU01 sp016926875	77.3059	363	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JAFGNU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056405.1	s__UBA2029 sp018056405	77.2611	302	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__UBA2029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002332795.1	s__UBA2029 sp002332795	77.0271	293	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__UBA2029	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010092855.1	s__TC-15 sp010092855	76.8757	296	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__TC-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934195.1	s__JAFGTJ01 sp016934195	76.8512	261	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JAFGTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234525.1	s__JACRBK01 sp016234525	76.2331	163	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JACRBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930015.1	s__JAFGHR01 sp016930015	76.1936	252	2065	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__Aggregatilineaceae;g__JAFGHR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:05,875] [INFO] GTDB search result was written to GCF_003569045.1_Grel_assembly01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:05,875] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:05,879] [INFO] DFAST_QC result json was written to GCF_003569045.1_Grel_assembly01_genomic.fna/dqc_result.json
[2024-01-24 13:51:05,880] [INFO] DFAST_QC completed!
[2024-01-24 13:51:05,880] [INFO] Total running time: 0h1m53s