[2024-01-24 10:47:40,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,960] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference
[2024-01-24 10:47:44,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg614b752c-cb64-4979-8773-b25303060ec3/GCF_007993795.1_ASM799379v1_genomic.fna.gz | prodigal -d GCF_007993795.1_ASM799379v1_genomic.fna/cds.fna -a GCF_007993795.1_ASM799379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:58,458] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:58,459] [INFO] Task started: HMMsearch
[2024-01-24 10:47:58,459] [INFO] Running command: hmmsearch --tblout GCF_007993795.1_ASM799379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference/reference_markers.hmm GCF_007993795.1_ASM799379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:58,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:58,724] [INFO] Found 6/6 markers.
[2024-01-24 10:47:58,752] [INFO] Query marker FASTA was written to GCF_007993795.1_ASM799379v1_genomic.fna/markers.fasta
[2024-01-24 10:47:58,753] [INFO] Task started: Blastn
[2024-01-24 10:47:58,753] [INFO] Running command: blastn -query GCF_007993795.1_ASM799379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference/reference_markers.fasta -out GCF_007993795.1_ASM799379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,422] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,425] [INFO] Selected 16 target genomes.
[2024-01-24 10:47:59,426] [INFO] Target genome list was writen to GCF_007993795.1_ASM799379v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:59,451] [INFO] Task started: fastANI
[2024-01-24 10:47:59,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg614b752c-cb64-4979-8773-b25303060ec3/GCF_007993795.1_ASM799379v1_genomic.fna.gz --refList GCF_007993795.1_ASM799379v1_genomic.fna/target_genomes.txt --output GCF_007993795.1_ASM799379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:10,454] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:10,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:10,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:10,467] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:10,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:10,467] [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
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	100.0	1136	1136	95	conclusive
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	78.792	410	1136	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	78.1862	344	1136	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	77.9375	185	1136	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	77.9175	202	1136	95	below_threshold
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	77.749	216	1136	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.6379	57	1136	95	below_threshold
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	77.5385	53	1136	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.3456	183	1136	95	below_threshold
Salegentibacter flavus	strain=DSM 17794	GCA_900115145.1	287099	287099	type	True	77.1149	174	1136	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	76.9879	210	1136	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.7207	121	1136	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	76.7161	164	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:10,469] [INFO] DFAST Taxonomy check result was written to GCF_007993795.1_ASM799379v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:10,470] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:10,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:10,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference/checkm_data
[2024-01-24 10:48:10,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:10,546] [INFO] Task started: CheckM
[2024-01-24 10:48:10,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007993795.1_ASM799379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007993795.1_ASM799379v1_genomic.fna/checkm_input GCF_007993795.1_ASM799379v1_genomic.fna/checkm_result
[2024-01-24 10:48:52,658] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:52,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:52,677] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:52,677] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:52,677] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007993795.1_ASM799379v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:52,678] [INFO] Task started: Blastn
[2024-01-24 10:48:52,678] [INFO] Running command: blastn -query GCF_007993795.1_ASM799379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ed14557-3a75-4701-b916-b37220637de6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007993795.1_ASM799379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:53,668] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:53,674] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:53,674] [INFO] Target genome list was writen to GCF_007993795.1_ASM799379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:53,717] [INFO] Task started: fastANI
[2024-01-24 10:48:53,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg614b752c-cb64-4979-8773-b25303060ec3/GCF_007993795.1_ASM799379v1_genomic.fna.gz --refList GCF_007993795.1_ASM799379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007993795.1_ASM799379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:05,592] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:05,609] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:05,609] [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_007993795.1	s__Gillisia arcticum	100.0	1136	1136	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_006159205.1	s__Gillisia flava	78.8646	412	1136	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	78.3701	216	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000243235.1	s__Gillisia limnaea	78.1862	344	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651535.1	s__Salinimicrobium marinum	77.9411	186	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	77.901	203	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827275.1	s__Gillisia sp007827275	77.802	241	1136	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	77.7309	218	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCA_002364325.1	s__Gillisia sp002364325	77.7089	168	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	77.6864	207	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403785.1	s__Gillisia sp000403785	77.5863	193	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003550275.1	s__QXCW01 sp003550275	77.2292	56	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__QXCW01	95.0	98.16	98.16	0.93	0.93	2	-
GCA_016649785.1	s__Gillisia sp016649785	77.2081	177	1136	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	76.964	212	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_003054225.1	s__Gramella gaetbulicola	76.7297	166	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.7236	122	1136	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:05,611] [INFO] GTDB search result was written to GCF_007993795.1_ASM799379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:05,611] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:05,615] [INFO] DFAST_QC result json was written to GCF_007993795.1_ASM799379v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:05,615] [INFO] DFAST_QC completed!
[2024-01-24 10:49:05,616] [INFO] Total running time: 0h1m25s