[2024-01-24 11:12:36,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,241] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,241] [INFO] DQC Reference Directory: /var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference
[2024-01-24 11:12:38,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,664] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,664] [INFO] Running command: gunzip -c /var/lib/cwl/stg9276acf5-1803-4382-a2ac-3d2cd2bb62d2/GCF_020164595.1_ASM2016459v1_genomic.fna.gz | prodigal -d GCF_020164595.1_ASM2016459v1_genomic.fna/cds.fna -a GCF_020164595.1_ASM2016459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:49,185] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:49,185] [INFO] Task started: HMMsearch
[2024-01-24 11:12:49,185] [INFO] Running command: hmmsearch --tblout GCF_020164595.1_ASM2016459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference/reference_markers.hmm GCF_020164595.1_ASM2016459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:49,388] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:49,389] [INFO] Found 6/6 markers.
[2024-01-24 11:12:49,414] [INFO] Query marker FASTA was written to GCF_020164595.1_ASM2016459v1_genomic.fna/markers.fasta
[2024-01-24 11:12:49,414] [INFO] Task started: Blastn
[2024-01-24 11:12:49,414] [INFO] Running command: blastn -query GCF_020164595.1_ASM2016459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference/reference_markers.fasta -out GCF_020164595.1_ASM2016459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:49,997] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:50,002] [INFO] Selected 17 target genomes.
[2024-01-24 11:12:50,002] [INFO] Target genome list was writen to GCF_020164595.1_ASM2016459v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:50,009] [INFO] Task started: fastANI
[2024-01-24 11:12:50,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg9276acf5-1803-4382-a2ac-3d2cd2bb62d2/GCF_020164595.1_ASM2016459v1_genomic.fna.gz --refList GCF_020164595.1_ASM2016459v1_genomic.fna/target_genomes.txt --output GCF_020164595.1_ASM2016459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:59,714] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:59,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:59,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:59,722] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:12:59,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:12:59,723] [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
Psychroflexus lacisalsi	strain=KACC 14089	GCA_020164495.1	503928	503928	type	True	88.9503	797	968	95	below_threshold
Psychroflexus sediminis	strain=DSM 19803	GCA_900099815.1	470826	470826	type	True	79.4352	492	968	95	below_threshold
Psychroflexus tropicus	strain=DSM 15496	GCA_000378765.1	197345	197345	type	True	78.6342	386	968	95	below_threshold
Psychroflexus aurantiacus	strain=YR1-1	GCA_010820555.1	2709310	2709310	type	True	78.6097	422	968	95	below_threshold
Psychroflexus gondwanensis	strain=ACAM 44	GCA_000355905.1	251	251	type	True	78.2091	349	968	95	below_threshold
Psychroflexus torquis	strain=ATCC 700755	GCA_000153485.2	57029	57029	type	True	77.8277	307	968	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.7049	56	968	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.371	56	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:59,725] [INFO] DFAST Taxonomy check result was written to GCF_020164595.1_ASM2016459v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:59,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:59,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:59,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference/checkm_data
[2024-01-24 11:12:59,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:59,757] [INFO] Task started: CheckM
[2024-01-24 11:12:59,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020164595.1_ASM2016459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020164595.1_ASM2016459v1_genomic.fna/checkm_input GCF_020164595.1_ASM2016459v1_genomic.fna/checkm_result
[2024-01-24 11:13:34,115] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:34,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:34,137] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:34,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:34,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020164595.1_ASM2016459v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:34,138] [INFO] Task started: Blastn
[2024-01-24 11:13:34,138] [INFO] Running command: blastn -query GCF_020164595.1_ASM2016459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde490976-545d-41ff-a10a-e34cde12faea/dqc_reference/reference_markers_gtdb.fasta -out GCF_020164595.1_ASM2016459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:34,950] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:34,953] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:34,953] [INFO] Target genome list was writen to GCF_020164595.1_ASM2016459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:34,966] [INFO] Task started: fastANI
[2024-01-24 11:13:34,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg9276acf5-1803-4382-a2ac-3d2cd2bb62d2/GCF_020164595.1_ASM2016459v1_genomic.fna.gz --refList GCF_020164595.1_ASM2016459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020164595.1_ASM2016459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:46,235] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:46,247] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:13:46,247] [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_900099815.1	s__Psychroflexus sediminis	79.4595	489	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378765.1	s__Psychroflexus tropicus	78.6342	386	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820555.1	s__Psychroflexus sp010820555	78.6142	421	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355905.1	s__Psychroflexus gondwanensis	78.2091	349	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	98.53	98.53	0.91	0.91	2	-
GCA_003565575.1	s__Psychroflexus sp003565575	78.0796	238	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836055.1	s__Psychroflexus sp002836055	77.8965	292	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153485.2	s__Psychroflexus torquis	77.827	307	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.7334	54	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002094855.1	s__Zunongwangia atlantica	76.7049	56	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430645.1	s__Aquimarina latercula	76.5642	50	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_014640195.1	s__Psychroflexus planctonicus	76.5182	105	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100805.1	s__Aquimarina sp018100805	76.4064	52	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.097	71	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964435.1	s__Mesonia sp012964435	76.0947	57	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:46,249] [INFO] GTDB search result was written to GCF_020164595.1_ASM2016459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:46,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:46,252] [INFO] DFAST_QC result json was written to GCF_020164595.1_ASM2016459v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:46,252] [INFO] DFAST_QC completed!
[2024-01-24 11:13:46,252] [INFO] Total running time: 0h1m10s