[2024-01-24 11:05:34,546] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:34,548] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:34,548] [INFO] DQC Reference Directory: /var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference
[2024-01-24 11:05:35,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:35,759] [INFO] Task started: Prodigal
[2024-01-24 11:05:35,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d7b41f0-6051-4cbd-9075-12c9c577c7eb/GCF_014636235.1_ASM1463623v1_genomic.fna.gz | prodigal -d GCF_014636235.1_ASM1463623v1_genomic.fna/cds.fna -a GCF_014636235.1_ASM1463623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:53,097] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:53,098] [INFO] Task started: HMMsearch
[2024-01-24 11:05:53,098] [INFO] Running command: hmmsearch --tblout GCF_014636235.1_ASM1463623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference/reference_markers.hmm GCF_014636235.1_ASM1463623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:53,458] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:53,460] [INFO] Found 6/6 markers.
[2024-01-24 11:05:53,511] [INFO] Query marker FASTA was written to GCF_014636235.1_ASM1463623v1_genomic.fna/markers.fasta
[2024-01-24 11:05:53,512] [INFO] Task started: Blastn
[2024-01-24 11:05:53,512] [INFO] Running command: blastn -query GCF_014636235.1_ASM1463623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference/reference_markers.fasta -out GCF_014636235.1_ASM1463623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:54,254] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:54,259] [INFO] Selected 27 target genomes.
[2024-01-24 11:05:54,259] [INFO] Target genome list was writen to GCF_014636235.1_ASM1463623v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:54,279] [INFO] Task started: fastANI
[2024-01-24 11:05:54,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7b41f0-6051-4cbd-9075-12c9c577c7eb/GCF_014636235.1_ASM1463623v1_genomic.fna.gz --refList GCF_014636235.1_ASM1463623v1_genomic.fna/target_genomes.txt --output GCF_014636235.1_ASM1463623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:18,116] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:18,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:18,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:18,149] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:18,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:18,150] [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
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	100.0	1803	1814	95	conclusive
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8573	266	1814	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.5882	312	1814	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5737	168	1814	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	76.5291	296	1814	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.4502	242	1814	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	76.4217	343	1814	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.4129	430	1814	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.4117	270	1814	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.3894	427	1814	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.2963	210	1814	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.1904	282	1814	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.18	353	1814	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.149	377	1814	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.1341	376	1814	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.1289	443	1814	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.1207	320	1814	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	76.1173	283	1814	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.1172	440	1814	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	76.1051	313	1814	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	76.0426	132	1814	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	76.0292	128	1814	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.9773	336	1814	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	75.7952	190	1814	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.6457	231	1814	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	75.6277	166	1814	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.5856	269	1814	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:18,152] [INFO] DFAST Taxonomy check result was written to GCF_014636235.1_ASM1463623v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:18,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:18,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:18,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference/checkm_data
[2024-01-24 11:06:18,154] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:18,218] [INFO] Task started: CheckM
[2024-01-24 11:06:18,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636235.1_ASM1463623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636235.1_ASM1463623v1_genomic.fna/checkm_input GCF_014636235.1_ASM1463623v1_genomic.fna/checkm_result
[2024-01-24 11:07:27,791] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:27,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:27,818] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:27,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:27,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636235.1_ASM1463623v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:27,819] [INFO] Task started: Blastn
[2024-01-24 11:07:27,819] [INFO] Running command: blastn -query GCF_014636235.1_ASM1463623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd01ccf3e-f4cc-432d-87d2-e8e20b26b145/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636235.1_ASM1463623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:28,993] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:28,998] [INFO] Selected 23 target genomes.
[2024-01-24 11:07:28,998] [INFO] Target genome list was writen to GCF_014636235.1_ASM1463623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:29,568] [INFO] Task started: fastANI
[2024-01-24 11:07:29,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d7b41f0-6051-4cbd-9075-12c9c577c7eb/GCF_014636235.1_ASM1463623v1_genomic.fna.gz --refList GCF_014636235.1_ASM1463623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636235.1_ASM1463623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:51,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:51,239] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:51,240] [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_014636235.1	s__Tistrella bauzanensis	100.0	1803	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000264455.2	s__Tistrella mobilis	83.3257	1376	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	96.38	95.97	0.88	0.84	5	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.7862	285	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941095.1	s__Magnetospirillum sp903941095	76.5515	217	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.83	99.83	0.93	0.93	2	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.4867	241	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	76.4351	427	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007197755.1	s__Ferrovibrio terrae	76.341	269	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	76.3223	258	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829825.1	s__Phaeospirillum magnetotacticum	76.2964	210	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.2889	366	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	76.2856	292	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_902729425.1	s__Phaeospirillum sp902729425	76.2583	276	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.2015	280	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.1639	354	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.1584	370	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	76.1484	441	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	76.0647	326	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	75.9718	334	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654615.1	s__Telmatospirillum sp015654615	75.9067	214	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793965.1	s__JAEULF01 sp016793965	75.7214	178	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULF01;f__JAEULF01;g__JAEULF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903835235.1	s__CAIMOR01 sp903835235	75.6288	344	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__CAIMOR01	95.0	99.98	99.96	0.99	0.98	6	-
GCA_003963125.1	s__AWTP1-13 sp003963125	75.6102	140	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355885.1	s__Roseococcus sp017355885	75.5716	184	1814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:51,242] [INFO] GTDB search result was written to GCF_014636235.1_ASM1463623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:51,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:51,247] [INFO] DFAST_QC result json was written to GCF_014636235.1_ASM1463623v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:51,247] [INFO] DFAST_QC completed!
[2024-01-24 11:07:51,248] [INFO] Total running time: 0h2m17s