[2024-01-24 12:36:58,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference
[2024-01-24 12:36:59,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,816] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,816] [INFO] Running command: gunzip -c /var/lib/cwl/stged4c593d-a354-4e7e-95b7-b4b87fc6e43b/GCF_003351045.1_ASM335104v1_genomic.fna.gz | prodigal -d GCF_003351045.1_ASM335104v1_genomic.fna/cds.fna -a GCF_003351045.1_ASM335104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:07,642] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:07,642] [INFO] Task started: HMMsearch
[2024-01-24 12:37:07,642] [INFO] Running command: hmmsearch --tblout GCF_003351045.1_ASM335104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference/reference_markers.hmm GCF_003351045.1_ASM335104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:07,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:07,948] [INFO] Found 6/6 markers.
[2024-01-24 12:37:07,976] [INFO] Query marker FASTA was written to GCF_003351045.1_ASM335104v1_genomic.fna/markers.fasta
[2024-01-24 12:37:07,976] [INFO] Task started: Blastn
[2024-01-24 12:37:07,976] [INFO] Running command: blastn -query GCF_003351045.1_ASM335104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference/reference_markers.fasta -out GCF_003351045.1_ASM335104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:08,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:08,858] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:08,858] [INFO] Target genome list was writen to GCF_003351045.1_ASM335104v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:08,925] [INFO] Task started: fastANI
[2024-01-24 12:37:08,925] [INFO] Running command: fastANI --query /var/lib/cwl/stged4c593d-a354-4e7e-95b7-b4b87fc6e43b/GCF_003351045.1_ASM335104v1_genomic.fna.gz --refList GCF_003351045.1_ASM335104v1_genomic.fna/target_genomes.txt --output GCF_003351045.1_ASM335104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:28,337] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:28,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:28,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:28,357] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:28,358] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:28,358] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	100.0	994	996	95	conclusive
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	76.0311	347	996	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	76.0113	267	996	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.9919	411	996	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.8879	256	996	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.8377	302	996	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.769	401	996	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	75.759	332	996	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	75.6769	290	996	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	75.458	150	996	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	75.2957	176	996	95	below_threshold
Pseudonocardia sulfidoxydans	strain=NBRC 16205	GCA_007989085.1	54011	54011	type	True	75.2373	247	996	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.1821	94	996	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	75.1417	150	996	95	below_threshold
Actinomadura latina	strain=ATCC BAA-277	GCA_012396395.1	163603	163603	type	True	75.1407	240	996	95	below_threshold
Actinomadura latina	strain=NBRC 106108	GCA_001552195.1	163603	163603	type	True	75.1224	237	996	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	75.1055	311	996	95	below_threshold
Asanoa ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	75.0423	220	996	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	75.0053	121	996	95	below_threshold
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	75.0045	217	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:28,360] [INFO] DFAST Taxonomy check result was written to GCF_003351045.1_ASM335104v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:28,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:28,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:28,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference/checkm_data
[2024-01-24 12:37:28,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:28,398] [INFO] Task started: CheckM
[2024-01-24 12:37:28,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003351045.1_ASM335104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003351045.1_ASM335104v1_genomic.fna/checkm_input GCF_003351045.1_ASM335104v1_genomic.fna/checkm_result
[2024-01-24 12:38:07,510] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:07,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:07,535] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:07,536] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:07,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003351045.1_ASM335104v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:07,537] [INFO] Task started: Blastn
[2024-01-24 12:38:07,537] [INFO] Running command: blastn -query GCF_003351045.1_ASM335104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73703d8c-8285-4c8b-8c96-29a1e7ff8256/dqc_reference/reference_markers_gtdb.fasta -out GCF_003351045.1_ASM335104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:08,682] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:08,686] [INFO] Selected 15 target genomes.
[2024-01-24 12:38:08,687] [INFO] Target genome list was writen to GCF_003351045.1_ASM335104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:08,744] [INFO] Task started: fastANI
[2024-01-24 12:38:08,745] [INFO] Running command: fastANI --query /var/lib/cwl/stged4c593d-a354-4e7e-95b7-b4b87fc6e43b/GCF_003351045.1_ASM335104v1_genomic.fna.gz --refList GCF_003351045.1_ASM335104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003351045.1_ASM335104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:17,461] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:17,476] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:17,476] [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_003351045.1	s__Gaiella occulta	100.0	994	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016870235.1	s__Gaiella sp016870235	79.7282	339	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694305.1	s__Gaiella sp009694305	79.4915	356	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366385.1	s__GMQP-bins7 sp004366385	78.9587	384	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__GMQP-bins7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694685.1	s__Gaiella sp013694685	78.8482	295	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Gaiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884575.1	s__AC-16 sp005884575	78.2962	418	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134505.1	s__PALSA-612 sp003134505	78.2403	327	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__PALSA-612	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236545.1	s__Palsa-739 sp019236545	78.2269	327	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	98.19	98.19	0.82	0.82	2	-
GCA_013696185.1	s__JACCZA01 sp013696185	78.1936	289	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCZA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139545.1	s__Palsa-739 sp003139545	78.0885	349	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__Palsa-739	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930195.1	s__PALSA-600 sp903930195	77.9641	224	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__PALSA-600	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884155.1	s__AC-32 sp005884155	77.9398	233	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812465.1	s__GMQP-bins7 sp013812465	77.7056	207	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__GMQP-bins7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844515.1	s__GMQP-bins7 sp016844515	77.6376	271	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__GMQP-bins7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885125.1	s__AC-21 sp005885125	77.4366	262	996	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-21	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:17,479] [INFO] GTDB search result was written to GCF_003351045.1_ASM335104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:17,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:17,485] [INFO] DFAST_QC result json was written to GCF_003351045.1_ASM335104v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:17,485] [INFO] DFAST_QC completed!
[2024-01-24 12:38:17,485] [INFO] Total running time: 0h1m19s