[2024-01-24 13:17:15,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference
[2024-01-24 13:17:17,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:17,097] [INFO] Task started: Prodigal
[2024-01-24 13:17:17,097] [INFO] Running command: gunzip -c /var/lib/cwl/stg096bd9c9-3f3a-4537-853f-128acd7c3c89/GCF_000243235.1_ASM24323v1_genomic.fna.gz | prodigal -d GCF_000243235.1_ASM24323v1_genomic.fna/cds.fna -a GCF_000243235.1_ASM24323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:33,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:33,143] [INFO] Task started: HMMsearch
[2024-01-24 13:17:33,143] [INFO] Running command: hmmsearch --tblout GCF_000243235.1_ASM24323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference/reference_markers.hmm GCF_000243235.1_ASM24323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:33,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:33,416] [INFO] Found 6/6 markers.
[2024-01-24 13:17:33,450] [INFO] Query marker FASTA was written to GCF_000243235.1_ASM24323v1_genomic.fna/markers.fasta
[2024-01-24 13:17:33,450] [INFO] Task started: Blastn
[2024-01-24 13:17:33,451] [INFO] Running command: blastn -query GCF_000243235.1_ASM24323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference/reference_markers.fasta -out GCF_000243235.1_ASM24323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:34,135] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:34,139] [INFO] Selected 18 target genomes.
[2024-01-24 13:17:34,140] [INFO] Target genome list was writen to GCF_000243235.1_ASM24323v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:34,148] [INFO] Task started: fastANI
[2024-01-24 13:17:34,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg096bd9c9-3f3a-4537-853f-128acd7c3c89/GCF_000243235.1_ASM24323v1_genomic.fna.gz --refList GCF_000243235.1_ASM24323v1_genomic.fna/target_genomes.txt --output GCF_000243235.1_ASM24323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:46,545] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:46,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:46,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:46,559] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:46,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:46,560] [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 limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	100.0	1319	1321	95	conclusive
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	79.947	370	1321	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	78.3548	328	1321	95	below_threshold
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	78.1262	315	1321	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	77.9744	300	1321	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	77.7376	259	1321	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	77.7237	280	1321	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	77.6253	244	1321	95	below_threshold
Salegentibacter sediminis	strain=K5023	GCA_002078605.1	1930251	1930251	type	True	77.1155	168	1321	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.0656	173	1321	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	76.7894	189	1321	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	76.777	189	1321	95	below_threshold
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	76.7588	153	1321	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	76.6899	52	1321	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.4603	148	1321	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.2403	62	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,561] [INFO] DFAST Taxonomy check result was written to GCF_000243235.1_ASM24323v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:46,561] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:46,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:46,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference/checkm_data
[2024-01-24 13:17:46,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:46,603] [INFO] Task started: CheckM
[2024-01-24 13:17:46,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000243235.1_ASM24323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000243235.1_ASM24323v1_genomic.fna/checkm_input GCF_000243235.1_ASM24323v1_genomic.fna/checkm_result
[2024-01-24 13:18:32,202] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:32,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:32,221] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:32,221] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:32,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000243235.1_ASM24323v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:32,222] [INFO] Task started: Blastn
[2024-01-24 13:18:32,222] [INFO] Running command: blastn -query GCF_000243235.1_ASM24323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f1f96a4-349f-4c92-8599-71cdcd2d130d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000243235.1_ASM24323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:33,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:33,092] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:33,092] [INFO] Target genome list was writen to GCF_000243235.1_ASM24323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:33,137] [INFO] Task started: fastANI
[2024-01-24 13:18:33,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg096bd9c9-3f3a-4537-853f-128acd7c3c89/GCF_000243235.1_ASM24323v1_genomic.fna.gz --refList GCF_000243235.1_ASM24323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000243235.1_ASM24323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:42,888] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:42,906] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:42,906] [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_000243235.1	s__Gillisia limnaea	100.0	1319	1321	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_007997295.1	s__Gillisia hiemivivida	79.9524	369	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_007993795.1	s__Gillisia arcticum	78.3624	326	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104765.1	s__Gillisia sp900104765	78.2961	279	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_007827275.1	s__Gillisia sp007827275	78.0945	322	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634585.1	s__Gillisia mitskevichiae	78.0887	318	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006159205.1	s__Gillisia flava	77.9492	297	1321	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	77.8432	228	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649785.1	s__Gillisia sp016649785	77.8409	271	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	77.7131	280	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	77.6975	259	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002078605.1	s__Salegentibacter sediminis	77.098	170	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651535.1	s__Salinimicrobium marinum	77.0914	175	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024155.1	s__Gramella fulva	76.8431	151	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129445.1	s__Salegentibacter echinorum	76.7889	188	1321	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,908] [INFO] GTDB search result was written to GCF_000243235.1_ASM24323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:42,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:42,912] [INFO] DFAST_QC result json was written to GCF_000243235.1_ASM24323v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:42,912] [INFO] DFAST_QC completed!
[2024-01-24 13:18:42,912] [INFO] Total running time: 0h1m27s