[2024-01-24 13:09:33,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference
[2024-01-24 13:09:35,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,106] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg12d36534-524f-4ffd-b73e-5ba4b0c41f92/GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/cds.fna -a GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:47,952] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:47,952] [INFO] Task started: HMMsearch
[2024-01-24 13:09:47,953] [INFO] Running command: hmmsearch --tblout GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference/reference_markers.hmm GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:48,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:48,213] [INFO] Found 6/6 markers.
[2024-01-24 13:09:48,262] [INFO] Query marker FASTA was written to GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:48,263] [INFO] Task started: Blastn
[2024-01-24 13:09:48,263] [INFO] Running command: blastn -query GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference/reference_markers.fasta -out GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:49,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:49,336] [INFO] Selected 23 target genomes.
[2024-01-24 13:09:49,336] [INFO] Target genome list was writen to GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:49,345] [INFO] Task started: fastANI
[2024-01-24 13:09:49,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg12d36534-524f-4ffd-b73e-5ba4b0c41f92/GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna.gz --refList GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:06,633] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:06,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:06,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:06,653] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:06,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:06,653] [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
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	100.0	1379	1381	95	conclusive
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	82.2398	726	1381	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	80.1528	725	1381	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.958	488	1381	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.863	449	1381	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.8219	444	1381	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.8149	524	1381	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.7885	427	1381	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	78.4135	432	1381	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.3433	409	1381	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0875	303	1381	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.0806	454	1381	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.021	394	1381	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.0045	325	1381	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.8884	378	1381	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.8658	375	1381	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	77.8341	339	1381	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.8317	383	1381	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8066	363	1381	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.8026	356	1381	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.7983	423	1381	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.5241	271	1381	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.2135	288	1381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:06,656] [INFO] DFAST Taxonomy check result was written to GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:06,656] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:06,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:06,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference/checkm_data
[2024-01-24 13:10:06,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:06,700] [INFO] Task started: CheckM
[2024-01-24 13:10:06,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/checkm_input GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:47,594] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:47,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:47,616] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:47,616] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:47,617] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:47,617] [INFO] Task started: Blastn
[2024-01-24 13:10:47,617] [INFO] Running command: blastn -query GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ac5f7a9-5f06-41e4-8c50-82c770cf3d22/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:49,517] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:49,521] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:49,521] [INFO] Target genome list was writen to GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:49,529] [INFO] Task started: fastANI
[2024-01-24 13:10:49,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg12d36534-524f-4ffd-b73e-5ba4b0c41f92/GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna.gz --refList GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:00,733] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:00,745] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:00,746] [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_900128995.1	s__Loktanella atrilutea	100.0	1379	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110065.1	s__Loktanella fryxellensis	82.2468	725	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145405.1	s__Loktanella sp004145405	80.4449	622	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114485.1	s__Loktanella salsilacus	80.1443	724	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_900110705.1	s__Loktanella sp900110705	79.0289	535	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	79.0115	544	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	78.789	427	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018263905.1	s__Loktanella sp018263905	78.7289	502	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	78.6163	468	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.3538	408	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	78.0497	371	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	77.9741	407	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_000526275.1	s__Lutimaribacter sp000526275	77.7713	391	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003646465.1	s__Chachezhania antarctica	77.5273	387	1381	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:00,747] [INFO] GTDB search result was written to GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:00,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:00,752] [INFO] DFAST_QC result json was written to GCF_900128995.1_IMG-taxon_2695420928_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:11:00,752] [INFO] DFAST_QC completed!
[2024-01-24 13:11:00,752] [INFO] Total running time: 0h1m27s