[2024-01-24 13:57:27,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:27,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:27,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference
[2024-01-24 13:57:28,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:28,523] [INFO] Task started: Prodigal
[2024-01-24 13:57:28,523] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9bcbf51-7389-449c-84c8-199733887f13/GCF_000258765.1_CBA3202_1.0_genomic.fna.gz | prodigal -d GCF_000258765.1_CBA3202_1.0_genomic.fna/cds.fna -a GCF_000258765.1_CBA3202_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:38,119] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:38,119] [INFO] Task started: HMMsearch
[2024-01-24 13:57:38,119] [INFO] Running command: hmmsearch --tblout GCF_000258765.1_CBA3202_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference/reference_markers.hmm GCF_000258765.1_CBA3202_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:38,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:38,409] [INFO] Found 6/6 markers.
[2024-01-24 13:57:38,442] [INFO] Query marker FASTA was written to GCF_000258765.1_CBA3202_1.0_genomic.fna/markers.fasta
[2024-01-24 13:57:38,443] [INFO] Task started: Blastn
[2024-01-24 13:57:38,443] [INFO] Running command: blastn -query GCF_000258765.1_CBA3202_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference/reference_markers.fasta -out GCF_000258765.1_CBA3202_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:39,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:39,117] [INFO] Selected 16 target genomes.
[2024-01-24 13:57:39,117] [INFO] Target genome list was writen to GCF_000258765.1_CBA3202_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:57:39,125] [INFO] Task started: fastANI
[2024-01-24 13:57:39,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9bcbf51-7389-449c-84c8-199733887f13/GCF_000258765.1_CBA3202_1.0_genomic.fna.gz --refList GCF_000258765.1_CBA3202_1.0_genomic.fna/target_genomes.txt --output GCF_000258765.1_CBA3202_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:53,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:53,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:53,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:53,998] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:53,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:53,998] [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
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	100.0	939	944	95	conclusive
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	83.3049	701	944	95	below_threshold
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	83.113	696	944	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	78.124	163	944	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	77.9569	260	944	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	77.8802	206	944	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	77.3039	192	944	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	77.2565	185	944	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.1086	133	944	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.1051	193	944	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	76.5667	84	944	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.5049	61	944	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	76.4953	129	944	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.371	67	944	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.315	75	944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,000] [INFO] DFAST Taxonomy check result was written to GCF_000258765.1_CBA3202_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:57:54,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:54,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:54,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference/checkm_data
[2024-01-24 13:57:54,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:54,032] [INFO] Task started: CheckM
[2024-01-24 13:57:54,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000258765.1_CBA3202_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000258765.1_CBA3202_1.0_genomic.fna/checkm_input GCF_000258765.1_CBA3202_1.0_genomic.fna/checkm_result
[2024-01-24 13:58:28,858] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:28,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:28,874] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:28,874] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:28,874] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000258765.1_CBA3202_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:58:28,874] [INFO] Task started: Blastn
[2024-01-24 13:58:28,874] [INFO] Running command: blastn -query GCF_000258765.1_CBA3202_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stg707cdea7-9ba1-407e-8b24-78453f505765/dqc_reference/reference_markers_gtdb.fasta -out GCF_000258765.1_CBA3202_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:29,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:29,772] [INFO] Selected 6 target genomes.
[2024-01-24 13:58:29,773] [INFO] Target genome list was writen to GCF_000258765.1_CBA3202_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:29,779] [INFO] Task started: fastANI
[2024-01-24 13:58:29,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9bcbf51-7389-449c-84c8-199733887f13/GCF_000258765.1_CBA3202_1.0_genomic.fna.gz --refList GCF_000258765.1_CBA3202_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_000258765.1_CBA3202_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:34,749] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:34,756] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:34,756] [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_000258765.1	s__Gillisia marina	100.0	939	944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007827275.1	s__Gillisia sp007827275	83.3589	699	944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997295.1	s__Gillisia hiemivivida	83.2922	702	944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_003634585.1	s__Gillisia mitskevichiae	83.1191	695	944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403785.1	s__Gillisia sp000403785	82.5154	688	944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364325.1	s__Gillisia sp002364325	80.6379	450	944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:34,757] [INFO] GTDB search result was written to GCF_000258765.1_CBA3202_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:34,758] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:34,761] [INFO] DFAST_QC result json was written to GCF_000258765.1_CBA3202_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:58:34,761] [INFO] DFAST_QC completed!
[2024-01-24 13:58:34,761] [INFO] Total running time: 0h1m7s