[2023-06-29 16:35:01,884] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:35:01,886] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:35:01,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference
[2023-06-29 16:35:03,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:35:03,114] [INFO] Task started: Prodigal
[2023-06-29 16:35:03,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf7eb502-f67e-4bb8-b4c6-32b1f203da07/GCA_021300435.1_ASM2130043v1_genomic.fna.gz | prodigal -d GCA_021300435.1_ASM2130043v1_genomic.fna/cds.fna -a GCA_021300435.1_ASM2130043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:35:13,041] [INFO] Task succeeded: Prodigal
[2023-06-29 16:35:13,042] [INFO] Task started: HMMsearch
[2023-06-29 16:35:13,042] [INFO] Running command: hmmsearch --tblout GCA_021300435.1_ASM2130043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference/reference_markers.hmm GCA_021300435.1_ASM2130043v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:35:13,242] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:35:13,243] [INFO] Found 6/6 markers.
[2023-06-29 16:35:13,266] [INFO] Query marker FASTA was written to GCA_021300435.1_ASM2130043v1_genomic.fna/markers.fasta
[2023-06-29 16:35:13,266] [INFO] Task started: Blastn
[2023-06-29 16:35:13,266] [INFO] Running command: blastn -query GCA_021300435.1_ASM2130043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference/reference_markers.fasta -out GCA_021300435.1_ASM2130043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:35:14,022] [INFO] Task succeeded: Blastn
[2023-06-29 16:35:14,025] [INFO] Selected 30 target genomes.
[2023-06-29 16:35:14,026] [INFO] Target genome list was writen to GCA_021300435.1_ASM2130043v1_genomic.fna/target_genomes.txt
[2023-06-29 16:35:14,028] [INFO] Task started: fastANI
[2023-06-29 16:35:14,028] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf7eb502-f67e-4bb8-b4c6-32b1f203da07/GCA_021300435.1_ASM2130043v1_genomic.fna.gz --refList GCA_021300435.1_ASM2130043v1_genomic.fna/target_genomes.txt --output GCA_021300435.1_ASM2130043v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:35:33,379] [INFO] Task succeeded: fastANI
[2023-06-29 16:35:33,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:35:33,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:35:33,399] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:35:33,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:35:33,400] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	77.3733	178	762	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.2749	160	762	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.0632	127	762	95	below_threshold
Rhodoferax bucti	strain=GSA243-2	GCA_005876985.1	2576305	2576305	type	True	76.9539	119	762	95	below_threshold
Rhodoferax saidenbachensis	strain=DSM 22694	GCA_001955715.1	1484693	1484693	type	True	76.9237	121	762	95	below_threshold
Rhodoferax fermentans	strain=DSM 10138	GCA_016583655.1	28066	28066	type	True	76.9227	111	762	95	below_threshold
Rhodoferax fermentans	strain=JCM 7819	GCA_002017865.1	28066	28066	type	True	76.8807	110	762	95	below_threshold
Rhodoferax saidenbachensis	strain=ED16	GCA_000498435.1	1484693	1484693	type	True	76.8682	120	762	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	76.6813	95	762	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	76.5962	109	762	95	below_threshold
Polaromonas eurypsychrophila	strain=CGMCC 1.15322	GCA_014641715.1	1614635	1614635	type	True	76.571	103	762	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	76.5601	94	762	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	76.557	86	762	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	76.5412	108	762	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	76.4294	66	762	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	76.4018	108	762	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	76.351	86	762	95	below_threshold
Malikia spinosa	strain=83	GCA_002980625.1	86180	86180	type	True	76.3486	57	762	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	76.3479	100	762	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	76.3165	93	762	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	76.2788	85	762	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.2091	84	762	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	76.117	100	762	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.087	73	762	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:35:33,402] [INFO] DFAST Taxonomy check result was written to GCA_021300435.1_ASM2130043v1_genomic.fna/tc_result.tsv
[2023-06-29 16:35:33,403] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:35:33,403] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:35:33,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference/checkm_data
[2023-06-29 16:35:33,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:35:33,431] [INFO] Task started: CheckM
[2023-06-29 16:35:33,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021300435.1_ASM2130043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021300435.1_ASM2130043v1_genomic.fna/checkm_input GCA_021300435.1_ASM2130043v1_genomic.fna/checkm_result
[2023-06-29 16:36:09,814] [INFO] Task succeeded: CheckM
[2023-06-29 16:36:09,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:36:09,828] [INFO] ===== Completeness check finished =====
[2023-06-29 16:36:09,829] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:36:09,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021300435.1_ASM2130043v1_genomic.fna/markers.fasta)
[2023-06-29 16:36:09,829] [INFO] Task started: Blastn
[2023-06-29 16:36:09,829] [INFO] Running command: blastn -query GCA_021300435.1_ASM2130043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34b40870-51fe-4bb8-bcce-9314d4d093f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_021300435.1_ASM2130043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:36:11,189] [INFO] Task succeeded: Blastn
[2023-06-29 16:36:11,192] [INFO] Selected 21 target genomes.
[2023-06-29 16:36:11,193] [INFO] Target genome list was writen to GCA_021300435.1_ASM2130043v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:36:11,197] [INFO] Task started: fastANI
[2023-06-29 16:36:11,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf7eb502-f67e-4bb8-b4c6-32b1f203da07/GCA_021300435.1_ASM2130043v1_genomic.fna.gz --refList GCA_021300435.1_ASM2130043v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021300435.1_ASM2130043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:36:22,107] [INFO] Task succeeded: fastANI
[2023-06-29 16:36:22,124] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:36:22,125] [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
GCA_005789825.1	s__Limnohabitans sp005789825	99.2302	558	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	96.68	96.68	0.84	0.84	2	conclusive
GCA_009925585.1	s__Limnohabitans sp009925585	82.308	516	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.01	99.01	0.84	0.84	2	-
GCA_903887325.1	s__Limnohabitans sp903887325	80.7826	436	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.65	99.44	0.91	0.87	5	-
GCA_009693225.1	s__Limnohabitans sp009693225	79.4584	280	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903956845.1	s__Limnohabitans sp903956845	79.1727	332	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969975.1	s__Limnohabitans sp018969975	78.1856	124	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009927495.1	s__Limnohabitans sp009927495	77.9635	179	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.87	98.87	0.69	0.69	2	-
GCF_002778315.1	s__Limnohabitans sp002778315	77.8748	200	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.08	98.08	0.92	0.92	2	-
GCA_903892175.1	s__Limnohabitans sp903892175	77.4839	183	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.61	96.75	0.84	0.82	4	-
GCA_903932865.1	s__Limnohabitans_A sp903932865	77.3224	155	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.93	99.93	0.98	0.98	2	-
GCF_003063455.1	s__Limnohabitans_A parvus	77.2924	159	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	77.2095	132	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848645.1	s__Limnohabitans_A sp017848645	77.2059	162	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCF_003063265.1	s__Limnohabitans_A sp003063265	76.8533	173	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.80	97.80	0.90	0.90	2	-
GCF_004795855.1	s__Hydrogenophaga sp004795855	76.8379	99	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925445.1	s__Limnohabitans sp903925445	76.6081	140	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844215.1	s__CAIKVZ01 sp903844215	76.5108	103	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463455.1	s__Rhodoferax sp016463455	76.4972	77	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	76.2766	90	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCA_009912175.1	s__Comamonas_F wautersii_A	76.1455	71	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948265.1	s__Rhodoferax sp017948265	76.1098	83	762	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:36:22,126] [INFO] GTDB search result was written to GCA_021300435.1_ASM2130043v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:36:22,127] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:36:22,132] [INFO] DFAST_QC result json was written to GCA_021300435.1_ASM2130043v1_genomic.fna/dqc_result.json
[2023-06-29 16:36:22,132] [INFO] DFAST_QC completed!
[2023-06-29 16:36:22,132] [INFO] Total running time: 0h1m20s