[2024-01-24 13:55:57,900] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:57,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:57,903] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference
[2024-01-24 13:55:59,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,097] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,098] [INFO] Running command: gunzip -c /var/lib/cwl/stgd92f238b-c9f1-4a3f-a32c-0fea76b097c4/GCF_000333015.1_ASM33301v1_genomic.fna.gz | prodigal -d GCF_000333015.1_ASM33301v1_genomic.fna/cds.fna -a GCF_000333015.1_ASM33301v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:11,832] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:11,832] [INFO] Task started: HMMsearch
[2024-01-24 13:56:11,832] [INFO] Running command: hmmsearch --tblout GCF_000333015.1_ASM33301v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference/reference_markers.hmm GCF_000333015.1_ASM33301v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:12,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:12,101] [INFO] Found 6/6 markers.
[2024-01-24 13:56:12,135] [INFO] Query marker FASTA was written to GCF_000333015.1_ASM33301v1_genomic.fna/markers.fasta
[2024-01-24 13:56:12,135] [INFO] Task started: Blastn
[2024-01-24 13:56:12,135] [INFO] Running command: blastn -query GCF_000333015.1_ASM33301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference/reference_markers.fasta -out GCF_000333015.1_ASM33301v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:13,280] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:13,284] [INFO] Selected 14 target genomes.
[2024-01-24 13:56:13,284] [INFO] Target genome list was writen to GCF_000333015.1_ASM33301v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:13,304] [INFO] Task started: fastANI
[2024-01-24 13:56:13,304] [INFO] Running command: fastANI --query /var/lib/cwl/stgd92f238b-c9f1-4a3f-a32c-0fea76b097c4/GCF_000333015.1_ASM33301v1_genomic.fna.gz --refList GCF_000333015.1_ASM33301v1_genomic.fna/target_genomes.txt --output GCF_000333015.1_ASM33301v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:24,369] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:24,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:24,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:24,386] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:56:24,386] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:24,386] [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
Gordonia hirsuta	strain=NBRC 16056	GCA_000333015.1	53427	53427	type	True	100.0	1123	1128	95	conclusive
Gordonia hirsuta	strain=DSM 44140	GCA_000420685.1	53427	53427	type	True	100.0	1123	1128	95	conclusive
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	79.5621	562	1128	95	below_threshold
Gordonia sihwensis	strain=NBRC 108236	GCA_000333035.1	173559	173559	type	True	79.3295	528	1128	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	79.3197	533	1128	95	below_threshold
Gordonia neofelifaecis	strain=NRRL B-59395	GCA_000192435.2	945692	945692	type	True	79.2438	551	1128	95	below_threshold
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	79.1813	520	1128	95	below_threshold
Gordonia crocea	strain=NBRC 107697	GCA_009932435.1	589162	589162	type	True	79.1306	468	1128	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	79.0962	530	1128	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	79.0888	507	1128	95	below_threshold
Gordonia malaquae	strain=DSM 45064	GCA_900105435.1	410332	410332	type	True	78.9877	458	1128	95	below_threshold
Gordonia namibiensis	strain=NBRC 108229	GCA_000298235.1	168480	168480	type	True	78.7526	456	1128	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	78.6609	439	1128	95	below_threshold
Gordonia rubripertincta	strain=ATCC 14352	GCA_012396225.1	36822	36822	type	True	78.6055	460	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:24,388] [INFO] DFAST Taxonomy check result was written to GCF_000333015.1_ASM33301v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:24,389] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:24,389] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:24,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference/checkm_data
[2024-01-24 13:56:24,390] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:24,425] [INFO] Task started: CheckM
[2024-01-24 13:56:24,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000333015.1_ASM33301v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000333015.1_ASM33301v1_genomic.fna/checkm_input GCF_000333015.1_ASM33301v1_genomic.fna/checkm_result
[2024-01-24 13:57:04,234] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:04,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:04,257] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:04,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:04,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000333015.1_ASM33301v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:04,259] [INFO] Task started: Blastn
[2024-01-24 13:57:04,259] [INFO] Running command: blastn -query GCF_000333015.1_ASM33301v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2c8ef43-f09e-476b-a135-ccedda8276a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000333015.1_ASM33301v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:06,021] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:06,026] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:06,026] [INFO] Target genome list was writen to GCF_000333015.1_ASM33301v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:06,040] [INFO] Task started: fastANI
[2024-01-24 13:57:06,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgd92f238b-c9f1-4a3f-a32c-0fea76b097c4/GCF_000333015.1_ASM33301v1_genomic.fna.gz --refList GCF_000333015.1_ASM33301v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000333015.1_ASM33301v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:17,458] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:17,475] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:17,475] [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_000333015.1	s__Gordonia hirsuta	100.0	1123	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002993285.1	s__Gordonia iterans	80.918	745	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305675.1	s__Gordonia phthalatica	79.5309	566	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197435.1	s__Gordonia humi	79.3196	533	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333035.1	s__Gordonia sihwensis	79.3149	530	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	-
GCF_000192435.1	s__Gordonia neofelifaecis	79.2266	553	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423025.1	s__Gordonia shandongensis	79.1904	519	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932435.1	s__Gordonia crocea	79.132	468	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592365.1	s__Gordonia hydrophobica	79.0875	531	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009932475.1	s__Gordonia spumicola	79.0616	510	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344135.1	s__Gordonia malaquae	78.9359	457	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000298235.1	s__Gordonia namibiensis	78.7348	457	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.13	97.13	0.90	0.90	2	-
GCF_000327325.1	s__Gordonia rubripertincta	78.6449	442	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
GCF_017654315.1	s__Gordonia polyisoprenivorans_A	78.5353	471	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:17,476] [INFO] GTDB search result was written to GCF_000333015.1_ASM33301v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:17,477] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:17,480] [INFO] DFAST_QC result json was written to GCF_000333015.1_ASM33301v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:17,480] [INFO] DFAST_QC completed!
[2024-01-24 13:57:17,481] [INFO] Total running time: 0h1m20s