[2024-01-24 11:51:06,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference
[2024-01-24 11:51:07,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:07,640] [INFO] Task started: Prodigal
[2024-01-24 11:51:07,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0cae240-a307-4f95-baa3-eb6c798c82cb/GCF_005144635.2_ASM514463v2_genomic.fna.gz | prodigal -d GCF_005144635.2_ASM514463v2_genomic.fna/cds.fna -a GCF_005144635.2_ASM514463v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:43,247] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:43,248] [INFO] Task started: HMMsearch
[2024-01-24 11:51:43,248] [INFO] Running command: hmmsearch --tblout GCF_005144635.2_ASM514463v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference/reference_markers.hmm GCF_005144635.2_ASM514463v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:43,847] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:43,849] [INFO] Found 6/6 markers.
[2024-01-24 11:51:43,944] [INFO] Query marker FASTA was written to GCF_005144635.2_ASM514463v2_genomic.fna/markers.fasta
[2024-01-24 11:51:43,945] [INFO] Task started: Blastn
[2024-01-24 11:51:43,945] [INFO] Running command: blastn -query GCF_005144635.2_ASM514463v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference/reference_markers.fasta -out GCF_005144635.2_ASM514463v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:44,735] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:44,738] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:44,738] [INFO] Target genome list was writen to GCF_005144635.2_ASM514463v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:44,755] [INFO] Task started: fastANI
[2024-01-24 11:51:44,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cae240-a307-4f95-baa3-eb6c798c82cb/GCF_005144635.2_ASM514463v2_genomic.fna.gz --refList GCF_005144635.2_ASM514463v2_genomic.fna/target_genomes.txt --output GCF_005144635.2_ASM514463v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:18,450] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:18,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:18,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:18,472] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:52:18,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:18,472] [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 aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	100.0	4105	4106	95	conclusive
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	80.8312	2075	4106	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	80.5228	2132	4106	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	77.0049	961	4106	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	76.1343	683	4106	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.4577	1226	4106	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.17	950	4106	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1671	727	4106	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.1151	936	4106	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	74.9851	211	4106	95	below_threshold
Agromyces laixinhei	strain=HY052	GCA_006337065.1	2585717	2585717	type	True	74.9073	234	4106	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.8897	524	4106	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	74.8839	341	4106	95	below_threshold
Tepidiphilus margaritifer	strain=DSM 15129	GCA_000425565.1	203471	203471	type	True	74.8711	107	4106	95	below_threshold
Bifidobacterium choerinum	strain=DSM 20434	GCA_000484675.1	35760	35760	type	True	74.8662	131	4106	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	74.8602	356	4106	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	74.8047	465	4106	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	74.7908	317	4106	95	below_threshold
Georgenia ruanii	strain=JCM 15130	GCA_009193175.1	348442	348442	type	True	74.7658	355	4106	95	below_threshold
Bifidobacterium platyrrhinorum	strain=SMA15	GCA_010667645.1	2661628	2661628	type	True	74.7571	127	4106	95	below_threshold
Bifidobacterium phasiani	strain=6T3	GCA_019331775.1	2834431	2834431	type	True	74.753	153	4106	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	74.6655	110	4106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:18,475] [INFO] DFAST Taxonomy check result was written to GCF_005144635.2_ASM514463v2_genomic.fna/tc_result.tsv
[2024-01-24 11:52:18,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:18,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:18,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference/checkm_data
[2024-01-24 11:52:18,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:18,587] [INFO] Task started: CheckM
[2024-01-24 11:52:18,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005144635.2_ASM514463v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005144635.2_ASM514463v2_genomic.fna/checkm_input GCF_005144635.2_ASM514463v2_genomic.fna/checkm_result
[2024-01-24 11:55:21,639] [INFO] Task succeeded: CheckM
[2024-01-24 11:55:21,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:55:21,672] [INFO] ===== Completeness check finished =====
[2024-01-24 11:55:21,673] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:55:21,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005144635.2_ASM514463v2_genomic.fna/markers.fasta)
[2024-01-24 11:55:21,674] [INFO] Task started: Blastn
[2024-01-24 11:55:21,674] [INFO] Running command: blastn -query GCF_005144635.2_ASM514463v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg895f4ff8-d9a5-4c8b-9a69-2209a5c0270a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005144635.2_ASM514463v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:55:22,961] [INFO] Task succeeded: Blastn
[2024-01-24 11:55:22,966] [INFO] Selected 16 target genomes.
[2024-01-24 11:55:22,966] [INFO] Target genome list was writen to GCF_005144635.2_ASM514463v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:55:22,980] [INFO] Task started: fastANI
[2024-01-24 11:55:22,980] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0cae240-a307-4f95-baa3-eb6c798c82cb/GCF_005144635.2_ASM514463v2_genomic.fna.gz --refList GCF_005144635.2_ASM514463v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005144635.2_ASM514463v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:56:01,921] [INFO] Task succeeded: fastANI
[2024-01-24 11:56:01,939] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:56:01,939] [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_005144635.1	s__Polyangium sp005144635	99.9923	4060	4106	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_009649845.1	s__Polyangium spumosum	80.8464	2072	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144585.1	s__Polyangium fumosum	80.5287	2129	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001312805.1	s__Byssovorax cruenta	80.2666	59	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Byssovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	77.5055	1434	4106	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	77.5006	1622	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_903906315.1	s__CAIVJW01 sp903906315	77.49	1207	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	77.4781	1613	4106	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	77.377	1478	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	77.284	1480	4106	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	77.0272	1127	4106	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	76.6242	691	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361525.1	s__CAITIQ01 sp013361525	76.2201	782	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212965.1	s__JACRDA01 sp016212965	75.9896	1077	4106	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACRDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916195.1	s__CAIVQB01 sp903916195	74.8836	186	4106	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__CAIVQB01	95.0	99.38	98.88	0.92	0.89	6	-
GCF_000425565.1	s__Tepidiphilus margaritifer	74.8631	109	4106	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:56:01,941] [INFO] GTDB search result was written to GCF_005144635.2_ASM514463v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:56:01,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:56:01,946] [INFO] DFAST_QC result json was written to GCF_005144635.2_ASM514463v2_genomic.fna/dqc_result.json
[2024-01-24 11:56:01,946] [INFO] DFAST_QC completed!
[2024-01-24 11:56:01,946] [INFO] Total running time: 0h4m56s