[2024-01-24 11:20:18,239] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:18,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:18,241] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference
[2024-01-24 11:20:19,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:19,494] [INFO] Task started: Prodigal
[2024-01-24 11:20:19,494] [INFO] Running command: gunzip -c /var/lib/cwl/stg580ef972-1d6b-4037-abc7-f9eb4966c8e0/GCF_021568705.1_ASM2156870v1_genomic.fna.gz | prodigal -d GCF_021568705.1_ASM2156870v1_genomic.fna/cds.fna -a GCF_021568705.1_ASM2156870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:30,356] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:30,357] [INFO] Task started: HMMsearch
[2024-01-24 11:20:30,357] [INFO] Running command: hmmsearch --tblout GCF_021568705.1_ASM2156870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference/reference_markers.hmm GCF_021568705.1_ASM2156870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:30,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:30,675] [INFO] Found 6/6 markers.
[2024-01-24 11:20:30,708] [INFO] Query marker FASTA was written to GCF_021568705.1_ASM2156870v1_genomic.fna/markers.fasta
[2024-01-24 11:20:30,709] [INFO] Task started: Blastn
[2024-01-24 11:20:30,709] [INFO] Running command: blastn -query GCF_021568705.1_ASM2156870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference/reference_markers.fasta -out GCF_021568705.1_ASM2156870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:31,363] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:31,367] [INFO] Selected 22 target genomes.
[2024-01-24 11:20:31,368] [INFO] Target genome list was writen to GCF_021568705.1_ASM2156870v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:31,391] [INFO] Task started: fastANI
[2024-01-24 11:20:31,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg580ef972-1d6b-4037-abc7-f9eb4966c8e0/GCF_021568705.1_ASM2156870v1_genomic.fna.gz --refList GCF_021568705.1_ASM2156870v1_genomic.fna/target_genomes.txt --output GCF_021568705.1_ASM2156870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:44,707] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:44,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:44,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:44,736] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:44,736] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:44,736] [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	78.5445	303	1051	95	below_threshold
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	78.5037	369	1051	95	below_threshold
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	78.2381	319	1051	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	77.9392	223	1051	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	77.8627	282	1051	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	77.6656	186	1051	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.6218	185	1051	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_001752425.1	435906	435906	type	True	77.6094	185	1051	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.4012	177	1051	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	77.3652	225	1051	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	77.3242	180	1051	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.3131	179	1051	95	below_threshold
Salegentibacter mishustinae	strain=KCTC 12263	GCA_014651335.1	270918	270918	type	True	77.239	229	1051	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.158	147	1051	95	below_threshold
Flavobacterium oncorhynchi	strain=CCUG 59446	GCA_002217355.1	728056	728056	type	True	77.0179	53	1051	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.7392	102	1051	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.5601	83	1051	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.4484	52	1051	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	76.3901	63	1051	95	below_threshold
Flavobacterium plurextorum	strain=CCUG 60112	GCA_002217395.1	1114867	1114867	type	True	76.2651	77	1051	95	below_threshold
Flavobacterium quisquiliarum	strain=EA-12	GCA_019308285.1	1834436	1834436	type	True	76.2513	68	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:44,738] [INFO] DFAST Taxonomy check result was written to GCF_021568705.1_ASM2156870v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:44,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:44,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:44,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference/checkm_data
[2024-01-24 11:20:44,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:44,773] [INFO] Task started: CheckM
[2024-01-24 11:20:44,774] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021568705.1_ASM2156870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021568705.1_ASM2156870v1_genomic.fna/checkm_input GCF_021568705.1_ASM2156870v1_genomic.fna/checkm_result
[2024-01-24 11:21:20,753] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:20,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:20,776] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:20,776] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:20,777] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021568705.1_ASM2156870v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:20,777] [INFO] Task started: Blastn
[2024-01-24 11:21:20,777] [INFO] Running command: blastn -query GCF_021568705.1_ASM2156870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b742df4-a164-48fa-9f27-277ad1379466/dqc_reference/reference_markers_gtdb.fasta -out GCF_021568705.1_ASM2156870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:21,660] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:21,665] [INFO] Selected 19 target genomes.
[2024-01-24 11:21:21,665] [INFO] Target genome list was writen to GCF_021568705.1_ASM2156870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:21,682] [INFO] Task started: fastANI
[2024-01-24 11:21:21,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg580ef972-1d6b-4037-abc7-f9eb4966c8e0/GCF_021568705.1_ASM2156870v1_genomic.fna.gz --refList GCF_021568705.1_ASM2156870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021568705.1_ASM2156870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:33,441] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:33,460] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:33,460] [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_900104765.1	s__Gillisia sp900104765	78.6823	356	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000258765.1	s__Gillisia marina	78.5521	301	1051	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	78.4974	368	1051	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	78.2139	320	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_007827275.1	s__Gillisia sp007827275	78.1475	309	1051	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	78.1144	247	1051	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	78.076	328	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243235.1	s__Gillisia limnaea	77.8963	278	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	77.6485	187	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCA_016649785.1	s__Gillisia sp016649785	77.4198	172	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	77.4045	204	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900168045.1	s__Salegentibacter holothuriorum	77.3441	178	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900095.1	s__Salegentibacter mishustinae	77.34	227	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_016236915.1	s__Salegentibacter maritimus	77.2283	187	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_002217355.1	s__Flavobacterium oncorhynchi	77.0179	53	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.71	96.71	0.90	0.90	2	-
GCF_002303885.1	s__Flavobacterium sp002303885	76.6915	57	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370685.1	s__Aquimarina sp008370685	76.4581	94	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217395.1	s__Flavobacterium plurextorum	76.2569	76	1051	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.27	98.27	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:33,462] [INFO] GTDB search result was written to GCF_021568705.1_ASM2156870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:33,463] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:33,467] [INFO] DFAST_QC result json was written to GCF_021568705.1_ASM2156870v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:33,467] [INFO] DFAST_QC completed!
[2024-01-24 11:21:33,467] [INFO] Total running time: 0h1m15s