[2023-03-18 01:26:26,334] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference
[2023-03-18 01:26:27,522] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,522] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,522] [INFO] Running command: cat /var/lib/cwl/stg7b8f4f49-93e5-4000-8e9f-d1ef3d1504c1/OceanDNA-b33381.fa | prodigal -d OceanDNA-b33381/cds.fna -a OceanDNA-b33381/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:44,707] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:44,707] [INFO] Task started: HMMsearch
[2023-03-18 01:26:44,707] [INFO] Running command: hmmsearch --tblout OceanDNA-b33381/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference/reference_markers.hmm OceanDNA-b33381/protein.faa > /dev/null
[2023-03-18 01:26:44,964] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:44,965] [INFO] Found 6/6 markers.
[2023-03-18 01:26:44,988] [INFO] Query marker FASTA was written to OceanDNA-b33381/markers.fasta
[2023-03-18 01:26:44,990] [INFO] Task started: Blastn
[2023-03-18 01:26:44,990] [INFO] Running command: blastn -query OceanDNA-b33381/markers.fasta -db /var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference/reference_markers.fasta -out OceanDNA-b33381/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:45,769] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:45,770] [INFO] Selected 26 target genomes.
[2023-03-18 01:26:45,770] [INFO] Target genome list was writen to OceanDNA-b33381/target_genomes.txt
[2023-03-18 01:26:45,858] [INFO] Task started: fastANI
[2023-03-18 01:26:45,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b8f4f49-93e5-4000-8e9f-d1ef3d1504c1/OceanDNA-b33381.fa --refList OceanDNA-b33381/target_genomes.txt --output OceanDNA-b33381/fastani_result.tsv --threads 1
[2023-03-18 01:27:04,863] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:04,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:27:04,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:27:04,879] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:27:04,879] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:27:04,880] [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	78.3626	264	757	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	78.2454	229	757	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	78.0225	275	757	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.897	224	757	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.5271	209	757	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.5227	205	757	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.3625	211	757	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	77.3289	185	757	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	77.3089	170	757	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	77.3048	172	757	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	77.2945	171	757	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	77.2525	190	757	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	77.1985	177	757	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.1439	165	757	95	below_threshold
Tepidicella baoligensis	strain=B18-50	GCA_013432195.1	2707016	2707016	type	True	77.1435	137	757	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	77.1376	165	757	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.1077	152	757	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	77.0849	155	757	95	below_threshold
Polaromonas naphthalenivorans	strain=CJ2	GCA_000015505.1	216465	216465	type	True	76.9578	180	757	95	below_threshold
Brachymonas denitrificans	strain=DSM 15123	GCA_900110225.1	28220	28220	type	True	76.9325	116	757	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	76.9229	137	757	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	76.9097	149	757	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.8284	147	757	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	76.8186	139	757	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	76.8123	114	757	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	76.7695	147	757	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:27:04,880] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33381/tc_result.tsv
[2023-03-18 01:27:04,880] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:27:04,880] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:27:04,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference/checkm_data
[2023-03-18 01:27:04,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:27:04,885] [INFO] Task started: CheckM
[2023-03-18 01:27:04,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33381/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33381/checkm_input OceanDNA-b33381/checkm_result
[2023-03-18 01:28:02,069] [INFO] Task succeeded: CheckM
[2023-03-18 01:28:02,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:28:02,071] [INFO] ===== Completeness check finished =====
[2023-03-18 01:28:02,072] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:28:02,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33381/markers.fasta)
[2023-03-18 01:28:02,072] [INFO] Task started: Blastn
[2023-03-18 01:28:02,073] [INFO] Running command: blastn -query OceanDNA-b33381/markers.fasta -db /var/lib/cwl/stg98ebb745-3c6b-4981-88c0-8ea68c354c12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33381/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:28:03,529] [INFO] Task succeeded: Blastn
[2023-03-18 01:28:03,530] [INFO] Selected 24 target genomes.
[2023-03-18 01:28:03,530] [INFO] Target genome list was writen to OceanDNA-b33381/target_genomes_gtdb.txt
[2023-03-18 01:28:03,658] [INFO] Task started: fastANI
[2023-03-18 01:28:03,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b8f4f49-93e5-4000-8e9f-d1ef3d1504c1/OceanDNA-b33381.fa --refList OceanDNA-b33381/target_genomes_gtdb.txt --output OceanDNA-b33381/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:28:16,171] [INFO] Task succeeded: fastANI
[2023-03-18 01:28:16,185] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:28:16,185] [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_903956845.1	s__Limnohabitans sp903956845	82.3118	448	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887325.1	s__Limnohabitans sp903887325	79.7835	383	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.65	99.44	0.91	0.87	5	-
GCA_009925585.1	s__Limnohabitans sp009925585	79.1621	339	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.01	99.01	0.84	0.84	2	-
GCA_009693225.1	s__Limnohabitans sp009693225	79.0089	253	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789825.1	s__Limnohabitans sp005789825	78.9421	317	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	96.68	96.68	0.84	0.84	2	-
GCA_009921465.1	s__Limnohabitans sp009921465	78.8059	135	757	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	78.8003	219	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.87	98.87	0.69	0.69	2	-
GCA_903832625.1	s__Limnohabitans sp903832625	78.679	268	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_002778315.1	s__Limnohabitans sp002778315	78.6369	280	757	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	78.5954	258	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.61	96.75	0.84	0.82	4	-
GCF_003063455.1	s__Limnohabitans_A parvus	78.2518	228	757	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_003063545.1	s__Limnohabitans sp003063545	78.2411	238	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256145.1	s__Limnohabitans_A sp002256145	78.1048	266	757	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_903916355.1	s__Limnohabitans_A sp903916355	78.0254	230	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.87	99.87	0.93	0.93	2	-
GCA_018882835.1	s__Limnohabitans sp018882835	77.9235	249	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255935.1	s__Limnohabitans_A sp002255935	77.9064	251	757	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_001412575.1	s__Limnohabitans_A sp001412575	77.7638	190	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCA_903960915.1	s__Rhodoferax sp903960915	77.5484	190	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	99.23	97.99	0.89	0.81	4	-
GCA_009928125.1	s__Limnohabitans_A sp009928125	77.336	128	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.84	98.65	0.83	0.81	5	-
GCF_003097105.1	s__Rhodoferax_B sp003097105	77.2097	190	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001714725.1	s__Acidovorax sp001714725	77.013	179	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	76.934	109	757	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_016463455.1	s__Rhodoferax sp016463455	76.8328	90	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789685.1	s__Limnohabitans_A sp005789685	76.6653	78	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:28:16,185] [INFO] GTDB search result was written to OceanDNA-b33381/result_gtdb.tsv
[2023-03-18 01:28:16,185] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:28:16,188] [INFO] DFAST_QC result json was written to OceanDNA-b33381/dqc_result.json
[2023-03-18 01:28:16,188] [INFO] DFAST_QC completed!
[2023-03-18 01:28:16,188] [INFO] Total running time: 0h1m50s