[2024-01-24 13:01:50,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:50,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:50,557] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference
[2024-01-24 13:01:51,808] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,809] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d34e04c-03f0-4208-8d26-50ec8a9304fd/GCF_009649845.1_ASM964984v1_genomic.fna.gz | prodigal -d GCF_009649845.1_ASM964984v1_genomic.fna/cds.fna -a GCF_009649845.1_ASM964984v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:21,855] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:21,856] [INFO] Task started: HMMsearch
[2024-01-24 13:02:21,856] [INFO] Running command: hmmsearch --tblout GCF_009649845.1_ASM964984v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference/reference_markers.hmm GCF_009649845.1_ASM964984v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:22,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:22,405] [INFO] Found 6/6 markers.
[2024-01-24 13:02:22,492] [INFO] Query marker FASTA was written to GCF_009649845.1_ASM964984v1_genomic.fna/markers.fasta
[2024-01-24 13:02:22,493] [INFO] Task started: Blastn
[2024-01-24 13:02:22,493] [INFO] Running command: blastn -query GCF_009649845.1_ASM964984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference/reference_markers.fasta -out GCF_009649845.1_ASM964984v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:23,269] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:23,274] [INFO] Selected 22 target genomes.
[2024-01-24 13:02:23,275] [INFO] Target genome list was writen to GCF_009649845.1_ASM964984v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:23,286] [INFO] Task started: fastANI
[2024-01-24 13:02:23,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d34e04c-03f0-4208-8d26-50ec8a9304fd/GCF_009649845.1_ASM964984v1_genomic.fna.gz --refList GCF_009649845.1_ASM964984v1_genomic.fna/target_genomes.txt --output GCF_009649845.1_ASM964984v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:01,162] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:01,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:01,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:01,183] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:03:01,183] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:03:01,184] [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
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	100.0	3554	3559	95	conclusive
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	88.1593	2882	3559	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	80.873	2061	3559	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	76.8544	875	3559	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.88	664	3559	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.5423	1042	3559	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	75.1934	376	3559	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.1279	896	3559	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.1002	872	3559	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.0993	570	3559	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.9657	229	3559	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	74.9411	325	3559	95	below_threshold
Bifidobacterium castoris	strain=2020B	GCA_003952025.1	2306972	2306972	type	True	74.8812	134	3559	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	74.8636	264	3559	95	below_threshold
Burkholderia singularis	strain=LMG 28154	GCA_900176645.1	1503053	1503053	type	True	74.8545	250	3559	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	74.8531	223	3559	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.8496	433	3559	95	below_threshold
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	74.8358	342	3559	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	74.8309	170	3559	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	74.8163	319	3559	95	below_threshold
Microbispora fusca	strain=NEAU-HEGS1-5	GCA_005864065.1	2576905	2576905	type	True	74.7888	352	3559	95	below_threshold
Pseudoclavibacter endophyticus	strain=CGMCC 1.15081	GCA_014640595.1	1778590	1778590	type	True	74.7882	203	3559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:01,185] [INFO] DFAST Taxonomy check result was written to GCF_009649845.1_ASM964984v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:01,186] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:01,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:01,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference/checkm_data
[2024-01-24 13:03:01,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:01,288] [INFO] Task started: CheckM
[2024-01-24 13:03:01,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009649845.1_ASM964984v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009649845.1_ASM964984v1_genomic.fna/checkm_input GCF_009649845.1_ASM964984v1_genomic.fna/checkm_result
[2024-01-24 13:05:01,952] [INFO] Task succeeded: CheckM
[2024-01-24 13:05:01,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:05:01,981] [INFO] ===== Completeness check finished =====
[2024-01-24 13:05:01,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:05:01,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009649845.1_ASM964984v1_genomic.fna/markers.fasta)
[2024-01-24 13:05:01,983] [INFO] Task started: Blastn
[2024-01-24 13:05:01,983] [INFO] Running command: blastn -query GCF_009649845.1_ASM964984v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf5b2cca-8bd0-4f30-9f0d-973ef7ee7fb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_009649845.1_ASM964984v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:05:03,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:05:03,198] [INFO] Selected 13 target genomes.
[2024-01-24 13:05:03,198] [INFO] Target genome list was writen to GCF_009649845.1_ASM964984v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:05:03,243] [INFO] Task started: fastANI
[2024-01-24 13:05:03,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d34e04c-03f0-4208-8d26-50ec8a9304fd/GCF_009649845.1_ASM964984v1_genomic.fna.gz --refList GCF_009649845.1_ASM964984v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009649845.1_ASM964984v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:05:39,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:05:39,027] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:05:39,027] [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_009649845.1	s__Polyangium spumosum	100.0	3554	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005144585.1	s__Polyangium fumosum	88.1522	2883	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	80.8438	2039	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	77.4882	1453	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	77.4652	1370	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	77.4581	1520	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCF_004135735.1	s__Sorangium cellulosum_F	77.4291	1352	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906315.1	s__CAIVJW01 sp903906315	77.3313	1164	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	77.1964	1362	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000601485.1	s__Chondromyces apiculatus	76.8628	960	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Chondromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	76.5321	620	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719945.1	s__CAITIQ01 sp016719945	76.2683	878	3559	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	99.43	99.43	0.95	0.95	2	-
GCA_003818495.1	s__UBA4615 sp003818495	74.7634	342	3559	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:05:39,029] [INFO] GTDB search result was written to GCF_009649845.1_ASM964984v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:05:39,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:05:39,033] [INFO] DFAST_QC result json was written to GCF_009649845.1_ASM964984v1_genomic.fna/dqc_result.json
[2024-01-24 13:05:39,033] [INFO] DFAST_QC completed!
[2024-01-24 13:05:39,033] [INFO] Total running time: 0h3m48s