[2024-01-24 12:29:18,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:18,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:18,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference
[2024-01-24 12:29:20,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:20,083] [INFO] Task started: Prodigal
[2024-01-24 12:29:20,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg40e8f221-b181-4927-8a91-e1e79d2a4a52/GCF_013036045.1_ASM1303604v1_genomic.fna.gz | prodigal -d GCF_013036045.1_ASM1303604v1_genomic.fna/cds.fna -a GCF_013036045.1_ASM1303604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:33,198] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:33,199] [INFO] Task started: HMMsearch
[2024-01-24 12:29:33,199] [INFO] Running command: hmmsearch --tblout GCF_013036045.1_ASM1303604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference/reference_markers.hmm GCF_013036045.1_ASM1303604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:33,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:33,541] [INFO] Found 6/6 markers.
[2024-01-24 12:29:33,590] [INFO] Query marker FASTA was written to GCF_013036045.1_ASM1303604v1_genomic.fna/markers.fasta
[2024-01-24 12:29:33,590] [INFO] Task started: Blastn
[2024-01-24 12:29:33,590] [INFO] Running command: blastn -query GCF_013036045.1_ASM1303604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference/reference_markers.fasta -out GCF_013036045.1_ASM1303604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:34,209] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:34,214] [INFO] Selected 26 target genomes.
[2024-01-24 12:29:34,215] [INFO] Target genome list was writen to GCF_013036045.1_ASM1303604v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:34,245] [INFO] Task started: fastANI
[2024-01-24 12:29:34,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e8f221-b181-4927-8a91-e1e79d2a4a52/GCF_013036045.1_ASM1303604v1_genomic.fna.gz --refList GCF_013036045.1_ASM1303604v1_genomic.fna/target_genomes.txt --output GCF_013036045.1_ASM1303604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:56,782] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:56,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:56,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:56,810] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:56,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:56,811] [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
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	100.0	1579	1594	95	conclusive
Alienimonas californiensis	strain=CA12	GCA_007743815.1	2527989	2527989	type	True	82.7878	1211	1594	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.8816	144	1594	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.8281	127	1594	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.8206	111	1594	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.2774	84	1594	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2227	184	1594	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0956	201	1594	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.0332	157	1594	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.0067	63	1594	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.0062	63	1594	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	74.7008	135	1594	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	74.691	89	1594	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	74.6644	118	1594	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	74.6454	115	1594	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.6232	144	1594	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	74.577	153	1594	95	below_threshold
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	74.569	60	1594	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:56,813] [INFO] DFAST Taxonomy check result was written to GCF_013036045.1_ASM1303604v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:56,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:56,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:56,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference/checkm_data
[2024-01-24 12:29:56,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:56,870] [INFO] Task started: CheckM
[2024-01-24 12:29:56,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013036045.1_ASM1303604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013036045.1_ASM1303604v1_genomic.fna/checkm_input GCF_013036045.1_ASM1303604v1_genomic.fna/checkm_result
[2024-01-24 12:30:36,056] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:36,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:36,077] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:36,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:36,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013036045.1_ASM1303604v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:36,078] [INFO] Task started: Blastn
[2024-01-24 12:30:36,078] [INFO] Running command: blastn -query GCF_013036045.1_ASM1303604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd59b583e-4d7f-4b4e-a61b-8b15d1eedc24/dqc_reference/reference_markers_gtdb.fasta -out GCF_013036045.1_ASM1303604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:37,060] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:37,065] [INFO] Selected 22 target genomes.
[2024-01-24 12:30:37,066] [INFO] Target genome list was writen to GCF_013036045.1_ASM1303604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:37,175] [INFO] Task started: fastANI
[2024-01-24 12:30:37,175] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e8f221-b181-4927-8a91-e1e79d2a4a52/GCF_013036045.1_ASM1303604v1_genomic.fna.gz --refList GCF_013036045.1_ASM1303604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013036045.1_ASM1303604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:57,010] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:57,026] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:57,027] [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_013036045.1	s__Alienimonas chondri	100.0	1579	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007743815.1	s__Alienimonas californiensis	82.8035	1210	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Alienimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007744515.1	s__Calycomorphotria sp007744515	76.171	90	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Calycomorphotria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.872	145	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.7974	175	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200145.1	s__JACQFH01 sp016200145	75.2435	91	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__JACQFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	75.2301	182	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124895.1	s__JABMPE01 sp016124895	75.1784	74	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABMPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861195.1	s__UBA10511 sp903861195	75.1452	58	1594	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__UBA10511	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696725.1	s__J020 sp003696725	75.0229	80	1594	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__J020	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	74.759	63	1594	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	74.6594	129	1594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_014648495.1	s__Spirillospora cremea	74.6568	208	1594	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912585.1	s__CAIXSE01 sp903912585	74.6201	50	1594	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__UBA2241;f__UBA2241;g__CAIXSE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	74.6097	142	1594	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,029] [INFO] GTDB search result was written to GCF_013036045.1_ASM1303604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:57,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:57,036] [INFO] DFAST_QC result json was written to GCF_013036045.1_ASM1303604v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:57,037] [INFO] DFAST_QC completed!
[2024-01-24 12:30:57,037] [INFO] Total running time: 0h1m38s