[2024-01-25 19:09:20,704] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference
[2024-01-25 19:09:21,881] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,882] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,882] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5b3bc7f-4228-41ad-a806-302a33eead7d/GCF_024054565.1_ASM2405456v1_genomic.fna.gz | prodigal -d GCF_024054565.1_ASM2405456v1_genomic.fna/cds.fna -a GCF_024054565.1_ASM2405456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:45,951] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:45,952] [INFO] Task started: HMMsearch
[2024-01-25 19:09:45,952] [INFO] Running command: hmmsearch --tblout GCF_024054565.1_ASM2405456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference/reference_markers.hmm GCF_024054565.1_ASM2405456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:46,273] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:46,274] [INFO] Found 6/6 markers.
[2024-01-25 19:09:46,331] [INFO] Query marker FASTA was written to GCF_024054565.1_ASM2405456v1_genomic.fna/markers.fasta
[2024-01-25 19:09:46,332] [INFO] Task started: Blastn
[2024-01-25 19:09:46,332] [INFO] Running command: blastn -query GCF_024054565.1_ASM2405456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference/reference_markers.fasta -out GCF_024054565.1_ASM2405456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:46,898] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:46,902] [INFO] Selected 21 target genomes.
[2024-01-25 19:09:46,902] [INFO] Target genome list was writen to GCF_024054565.1_ASM2405456v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:46,921] [INFO] Task started: fastANI
[2024-01-25 19:09:46,921] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5b3bc7f-4228-41ad-a806-302a33eead7d/GCF_024054565.1_ASM2405456v1_genomic.fna.gz --refList GCF_024054565.1_ASM2405456v1_genomic.fna/target_genomes.txt --output GCF_024054565.1_ASM2405456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:04,917] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:04,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:04,923] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:04,931] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:10:04,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:10:04,931] [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
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	77.5681	522	2553	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	77.1911	328	2553	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	77.122	328	2553	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.9678	257	2553	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.9049	266	2553	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.8036	211	2553	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.3084	158	2553	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.2898	184	2553	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.6828	67	2553	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	74.6955	57	2553	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	74.6542	50	2553	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:04,933] [INFO] DFAST Taxonomy check result was written to GCF_024054565.1_ASM2405456v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:04,934] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:04,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:04,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference/checkm_data
[2024-01-25 19:10:04,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:05,014] [INFO] Task started: CheckM
[2024-01-25 19:10:05,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024054565.1_ASM2405456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024054565.1_ASM2405456v1_genomic.fna/checkm_input GCF_024054565.1_ASM2405456v1_genomic.fna/checkm_result
[2024-01-25 19:11:10,074] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:10,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:10,096] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:10,096] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:10,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024054565.1_ASM2405456v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:10,098] [INFO] Task started: Blastn
[2024-01-25 19:11:10,098] [INFO] Running command: blastn -query GCF_024054565.1_ASM2405456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32f7aed2-1987-4f76-b3e0-93a0a72a47af/dqc_reference/reference_markers_gtdb.fasta -out GCF_024054565.1_ASM2405456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:10,943] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:10,946] [INFO] Selected 22 target genomes.
[2024-01-25 19:11:10,946] [INFO] Target genome list was writen to GCF_024054565.1_ASM2405456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:10,985] [INFO] Task started: fastANI
[2024-01-25 19:11:10,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5b3bc7f-4228-41ad-a806-302a33eead7d/GCF_024054565.1_ASM2405456v1_genomic.fna.gz --refList GCF_024054565.1_ASM2405456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024054565.1_ASM2405456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:33,263] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:33,273] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:11:33,273] [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_007748035.1	s__Aeoliella mucimassa	77.5635	522	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Aeoliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	77.208	326	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	77.1463	325	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	76.968	257	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	76.9049	266	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	76.8319	217	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859955.1	s__Botrimarina colliarenosi	76.8042	211	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	76.7979	278	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576855.1	s__Lacipirellula sp003576855	76.3398	153	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	76.3064	181	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	76.1811	115	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	75.8524	76	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515235.1	s__Anammoximicrobium sp012515235	75.5311	88	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anammoximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455945.1	s__UBA11682 sp003455945	75.0665	63	2553	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA11682	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796285.1	s__Streptomyces broussonetiae	74.6542	50	2553	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:33,274] [INFO] GTDB search result was written to GCF_024054565.1_ASM2405456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:33,275] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:33,278] [INFO] DFAST_QC result json was written to GCF_024054565.1_ASM2405456v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:33,278] [INFO] DFAST_QC completed!
[2024-01-25 19:11:33,278] [INFO] Total running time: 0h2m13s