[2023-03-17 08:31:46,166] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:31:46,167] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:31:46,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference
[2023-03-17 08:31:47,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:31:47,408] [INFO] Task started: Prodigal
[2023-03-17 08:31:47,409] [INFO] Running command: cat /var/lib/cwl/stg9d1c19c6-4f9b-4e28-9d01-467f0503f493/OceanDNA-b28585.fa | prodigal -d OceanDNA-b28585/cds.fna -a OceanDNA-b28585/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:32:03,184] [INFO] Task succeeded: Prodigal
[2023-03-17 08:32:03,185] [INFO] Task started: HMMsearch
[2023-03-17 08:32:03,185] [INFO] Running command: hmmsearch --tblout OceanDNA-b28585/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference/reference_markers.hmm OceanDNA-b28585/protein.faa > /dev/null
[2023-03-17 08:32:03,360] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:32:03,360] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d1c19c6-4f9b-4e28-9d01-467f0503f493/OceanDNA-b28585.fa]
[2023-03-17 08:32:03,377] [INFO] Query marker FASTA was written to OceanDNA-b28585/markers.fasta
[2023-03-17 08:32:03,378] [INFO] Task started: Blastn
[2023-03-17 08:32:03,378] [INFO] Running command: blastn -query OceanDNA-b28585/markers.fasta -db /var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference/reference_markers.fasta -out OceanDNA-b28585/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:32:03,965] [INFO] Task succeeded: Blastn
[2023-03-17 08:32:03,965] [INFO] Selected 26 target genomes.
[2023-03-17 08:32:03,966] [INFO] Target genome list was writen to OceanDNA-b28585/target_genomes.txt
[2023-03-17 08:32:04,367] [INFO] Task started: fastANI
[2023-03-17 08:32:04,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1c19c6-4f9b-4e28-9d01-467f0503f493/OceanDNA-b28585.fa --refList OceanDNA-b28585/target_genomes.txt --output OceanDNA-b28585/fastani_result.tsv --threads 1
[2023-03-17 08:32:19,633] [INFO] Task succeeded: fastANI
[2023-03-17 08:32:19,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:32:19,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:32:19,643] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:32:19,643] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:32:19,643] [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
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.4913	63	788	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	76.4206	69	788	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	76.4112	64	788	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.2889	51	788	95	below_threshold
Roseovarius albus	strain=CECT 7450	GCA_900172335.1	1247867	1247867	type	True	76.2547	64	788	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	76.2411	71	788	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	76.104	67	788	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	76.0882	54	788	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	76.024	60	788	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	75.8581	58	788	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	75.8177	60	788	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	75.8177	60	788	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	75.7226	72	788	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:32:19,643] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28585/tc_result.tsv
[2023-03-17 08:32:19,643] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:32:19,643] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:32:19,643] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference/checkm_data
[2023-03-17 08:32:19,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:32:19,768] [INFO] Task started: CheckM
[2023-03-17 08:32:19,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28585/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28585/checkm_input OceanDNA-b28585/checkm_result
[2023-03-17 08:33:01,294] [INFO] Task succeeded: CheckM
[2023-03-17 08:33:01,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:33:01,297] [INFO] ===== Completeness check finished =====
[2023-03-17 08:33:01,297] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:33:01,297] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28585/markers.fasta)
[2023-03-17 08:33:01,298] [INFO] Task started: Blastn
[2023-03-17 08:33:01,298] [INFO] Running command: blastn -query OceanDNA-b28585/markers.fasta -db /var/lib/cwl/stg4e4f81e6-e846-4ab4-ab01-a2f23458f6d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28585/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:33:02,214] [INFO] Task succeeded: Blastn
[2023-03-17 08:33:02,215] [INFO] Selected 15 target genomes.
[2023-03-17 08:33:02,215] [INFO] Target genome list was writen to OceanDNA-b28585/target_genomes_gtdb.txt
[2023-03-17 08:33:02,898] [INFO] Task started: fastANI
[2023-03-17 08:33:02,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1c19c6-4f9b-4e28-9d01-467f0503f493/OceanDNA-b28585.fa --refList OceanDNA-b28585/target_genomes_gtdb.txt --output OceanDNA-b28585/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:33:11,512] [INFO] Task succeeded: fastANI
[2023-03-17 08:33:11,519] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:33:11,520] [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_000472185.1	s__HIMB11 sp000472185	91.7078	727	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017852835.1	s__HIMB11 sp003486095	91.5536	604	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	98.02	97.17	0.82	0.75	18	-
GCA_018222665.1	s__HIMB11 sp018222665	91.4178	437	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920225.1	s__HIMB11 sp009920225	77.344	103	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920815.1	s__HIMB11 sp009920815	76.7372	111	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510135.1	s__LFER01 sp001510135	76.5165	63	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LFER01	95.0	98.63	96.26	0.85	0.78	7	-
GCF_900172335.1	s__Roseovarius albus	76.2848	63	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458215.1	s__Shimia thalassica	76.2315	70	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	96.93	96.93	0.94	0.94	2	-
GCF_017798205.1	s__Cognatishimia activa_A	76.2187	66	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352425.1	s__Profundibacter sp002352425	76.2045	55	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346865.1	s__Shimia isoporae	76.2039	50	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032005.1	s__Ruegeria atlantica_A	75.8262	50	788	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
--------------------------------------------------------------------------------
[2023-03-17 08:33:11,520] [INFO] GTDB search result was written to OceanDNA-b28585/result_gtdb.tsv
[2023-03-17 08:33:11,520] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:33:11,521] [INFO] DFAST_QC result json was written to OceanDNA-b28585/dqc_result.json
[2023-03-17 08:33:11,521] [INFO] DFAST_QC completed!
[2023-03-17 08:33:11,521] [INFO] Total running time: 0h1m25s