[2024-01-24 12:06:33,789] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:33,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:33,791] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference
[2024-01-24 12:06:35,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,143] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg65c57d37-4c26-4a4c-9eb7-68c8a87b921d/GCF_014635345.1_ASM1463534v1_genomic.fna.gz | prodigal -d GCF_014635345.1_ASM1463534v1_genomic.fna/cds.fna -a GCF_014635345.1_ASM1463534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:53,371] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:53,372] [INFO] Task started: HMMsearch
[2024-01-24 12:06:53,372] [INFO] Running command: hmmsearch --tblout GCF_014635345.1_ASM1463534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference/reference_markers.hmm GCF_014635345.1_ASM1463534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:53,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:53,660] [INFO] Found 6/6 markers.
[2024-01-24 12:06:53,710] [INFO] Query marker FASTA was written to GCF_014635345.1_ASM1463534v1_genomic.fna/markers.fasta
[2024-01-24 12:06:53,711] [INFO] Task started: Blastn
[2024-01-24 12:06:53,711] [INFO] Running command: blastn -query GCF_014635345.1_ASM1463534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference/reference_markers.fasta -out GCF_014635345.1_ASM1463534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:54,780] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:54,785] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:54,785] [INFO] Target genome list was writen to GCF_014635345.1_ASM1463534v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:54,793] [INFO] Task started: fastANI
[2024-01-24 12:06:54,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c57d37-4c26-4a4c-9eb7-68c8a87b921d/GCF_014635345.1_ASM1463534v1_genomic.fna.gz --refList GCF_014635345.1_ASM1463534v1_genomic.fna/target_genomes.txt --output GCF_014635345.1_ASM1463534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:12,400] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:12,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:12,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:12,418] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:12,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:12,419] [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
Rhodococcus trifolii	strain=CCM 7905	GCA_014635345.1	908250	908250	type	True	100.0	1755	1755	95	conclusive
Rhodococcus corynebacterioides	strain=NBRC 14404	GCA_001894765.1	53972	53972	suspected-type	True	79.5284	608	1755	95	below_threshold
Rhodococcus kroppenstedtii	strain=DSM 44908	GCA_900111805.1	293050	293050	type	True	79.5176	604	1755	95	below_threshold
Rhodococcus corynebacterioides	strain=DSM 20151	GCA_001646675.1	53972	53972	suspected-type	True	79.5082	579	1755	95	below_threshold
Rhodococcus kroppenstedtii	strain=DSM 44908	GCA_001646725.1	293050	293050	type	True	79.4567	583	1755	95	below_threshold
Rhodococcus fascians	strain=NBRC 12155	GCA_001894785.1	1828	1828	type	True	78.8703	572	1755	95	below_threshold
Rhodococcus fascians	strain=LMG 3623	GCA_000761055.1	1828	1828	type	True	78.8545	584	1755	95	below_threshold
Prescottella equi	strain=C 7	GCA_000473915.1	43767	43767	type	True	78.5087	456	1755	95	below_threshold
Prescottella equi	strain=NBRC 101255	GCA_001552575.1	43767	43767	type	True	78.4304	459	1755	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	78.4218	458	1755	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	78.4101	462	1755	95	below_threshold
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	78.1588	572	1755	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	78.1572	555	1755	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	78.1166	484	1755	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	78.0502	491	1755	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	77.5958	396	1755	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	77.5247	370	1755	95	below_threshold
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	77.3235	356	1755	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	77.2998	411	1755	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:12,420] [INFO] DFAST Taxonomy check result was written to GCF_014635345.1_ASM1463534v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:12,421] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:12,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:12,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference/checkm_data
[2024-01-24 12:07:12,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:12,477] [INFO] Task started: CheckM
[2024-01-24 12:07:12,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635345.1_ASM1463534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635345.1_ASM1463534v1_genomic.fna/checkm_input GCF_014635345.1_ASM1463534v1_genomic.fna/checkm_result
[2024-01-24 12:08:09,264] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:09,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:09,289] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:09,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:09,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635345.1_ASM1463534v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:09,290] [INFO] Task started: Blastn
[2024-01-24 12:08:09,290] [INFO] Running command: blastn -query GCF_014635345.1_ASM1463534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ece17b4-e25f-47f7-a91a-8e5fb1dbc325/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635345.1_ASM1463534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:10,835] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:10,839] [INFO] Selected 18 target genomes.
[2024-01-24 12:08:10,839] [INFO] Target genome list was writen to GCF_014635345.1_ASM1463534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:10,853] [INFO] Task started: fastANI
[2024-01-24 12:08:10,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c57d37-4c26-4a4c-9eb7-68c8a87b921d/GCF_014635345.1_ASM1463534v1_genomic.fna.gz --refList GCF_014635345.1_ASM1463534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635345.1_ASM1463534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:29,062] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:29,078] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:29,079] [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_014635345.1	s__Rhodococcus_C trifolii	100.0	1755	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000686025.1	s__Rhodococcus_C sp000686025	79.7211	733	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	97.13	95.65	0.89	0.88	5	-
GCF_001426185.1	s__Rhodococcus_C sp001426185	79.7093	735	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	99.01	98.03	0.95	0.90	3	-
GCF_001894765.1	s__Rhodococcus_C corynebacterioides	79.5274	608	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900111805.1	s__Rhodococcus_C kroppenstedtii	79.5094	605	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	98.58	98.00	0.94	0.91	5	-
GCF_000954115.1	s__Rhodococcus_B sp000954115	78.9334	611	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.19	0.90	0.89	13	-
GCF_001894785.1	s__Rhodococcus_B fascians	78.8728	573	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	97.73	95.09	0.88	0.82	43	-
GCF_000760735.1	s__Rhodococcus_B fascians_E	78.5265	556	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.84	98.47	0.88	0.82	19	-
GCF_001646645.1	s__Rhodococcus hoagii	78.4867	444	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_013348805.1	s__Rhodococcus sp003350365	78.3619	485	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_017168235.1	s__Rhodococcus_B sp001942265	78.3476	463	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.66	98.66	0.86	0.86	2	-
GCF_001647195.1	s__Rhodococcus_B sp001647195	78.2854	437	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396235.1	s__Rhodococcus opacus	78.1448	574	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
GCF_011058165.1	s__Rhodococcus aetherivorans	78.1264	482	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_013602415.1	s__Rhodococcus sp013602415	78.0182	430	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612805.1	s__Nocardia coubleae	77.9757	366	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	77.602	294	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
GCF_000523235.1	s__Nocardia nova_A	77.4787	352	1755	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:29,080] [INFO] GTDB search result was written to GCF_014635345.1_ASM1463534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:29,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:29,085] [INFO] DFAST_QC result json was written to GCF_014635345.1_ASM1463534v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:29,085] [INFO] DFAST_QC completed!
[2024-01-24 12:08:29,085] [INFO] Total running time: 0h1m55s