[2024-01-25 19:58:20,708] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:20,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:20,709] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference
[2024-01-25 19:58:21,833] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:21,833] [INFO] Task started: Prodigal
[2024-01-25 19:58:21,834] [INFO] Running command: gunzip -c /var/lib/cwl/stg54bee7c2-4f23-4ce5-9a8d-4104264330c0/GCF_003992595.1_ASM399259v1_genomic.fna.gz | prodigal -d GCF_003992595.1_ASM399259v1_genomic.fna/cds.fna -a GCF_003992595.1_ASM399259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:42,314] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:42,315] [INFO] Task started: HMMsearch
[2024-01-25 19:58:42,315] [INFO] Running command: hmmsearch --tblout GCF_003992595.1_ASM399259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference/reference_markers.hmm GCF_003992595.1_ASM399259v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:42,855] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:42,856] [INFO] Found 6/6 markers.
[2024-01-25 19:58:42,891] [INFO] Query marker FASTA was written to GCF_003992595.1_ASM399259v1_genomic.fna/markers.fasta
[2024-01-25 19:58:42,892] [INFO] Task started: Blastn
[2024-01-25 19:58:42,892] [INFO] Running command: blastn -query GCF_003992595.1_ASM399259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference/reference_markers.fasta -out GCF_003992595.1_ASM399259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:43,485] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:43,488] [INFO] Selected 12 target genomes.
[2024-01-25 19:58:43,488] [INFO] Target genome list was writen to GCF_003992595.1_ASM399259v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:43,492] [INFO] Task started: fastANI
[2024-01-25 19:58:43,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg54bee7c2-4f23-4ce5-9a8d-4104264330c0/GCF_003992595.1_ASM399259v1_genomic.fna.gz --refList GCF_003992595.1_ASM399259v1_genomic.fna/target_genomes.txt --output GCF_003992595.1_ASM399259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:53,708] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:53,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:53,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:53,717] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:53,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:53,717] [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
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	100.0	1391	1396	95	conclusive
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	83.5483	826	1396	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	83.3804	890	1396	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	83.0697	813	1396	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	82.9259	837	1396	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	82.6171	799	1396	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	82.5245	813	1396	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	82.2184	824	1396	95	below_threshold
Muricauda lutimaris	strain=KCTC 22173	GCA_003581615.1	475082	475082	type	True	82.1376	759	1396	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.8333	529	1396	95	below_threshold
Pelagihabitans pacificus	strain=TP-CH-4	GCA_009371985.2	2696054	2696054	type	True	76.8701	83	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:53,719] [INFO] DFAST Taxonomy check result was written to GCF_003992595.1_ASM399259v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:53,719] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:53,719] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:53,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference/checkm_data
[2024-01-25 19:58:53,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:53,778] [INFO] Task started: CheckM
[2024-01-25 19:58:53,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003992595.1_ASM399259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003992595.1_ASM399259v1_genomic.fna/checkm_input GCF_003992595.1_ASM399259v1_genomic.fna/checkm_result
[2024-01-25 19:59:51,736] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:51,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:51,753] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:51,753] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:51,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003992595.1_ASM399259v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:51,754] [INFO] Task started: Blastn
[2024-01-25 19:59:51,754] [INFO] Running command: blastn -query GCF_003992595.1_ASM399259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8ac6a14-2d19-4ea2-8c4f-4af4c4f3d21f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003992595.1_ASM399259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:52,626] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:52,629] [INFO] Selected 11 target genomes.
[2024-01-25 19:59:52,629] [INFO] Target genome list was writen to GCF_003992595.1_ASM399259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:52,639] [INFO] Task started: fastANI
[2024-01-25 19:59:52,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg54bee7c2-4f23-4ce5-9a8d-4104264330c0/GCF_003992595.1_ASM399259v1_genomic.fna.gz --refList GCF_003992595.1_ASM399259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003992595.1_ASM399259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:00:02,833] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:02,840] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:00:02,840] [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_003992595.1	s__Muricauda sp002452975	100.0	1390	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	conclusive
GCF_010468565.1	s__Muricauda sp010468565	83.654	871	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	83.5559	825	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	83.5412	787	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	83.3913	857	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313785.1	s__Muricauda sp002711825	83.3812	891	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_011068285.1	s__Muricauda sp011068285	82.9108	837	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	82.6052	800	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_000224085.1	s__Muricauda ruestringensis	82.2675	822	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	82.2062	725	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	82.0923	775	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:00:02,842] [INFO] GTDB search result was written to GCF_003992595.1_ASM399259v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:00:02,842] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:00:02,845] [INFO] DFAST_QC result json was written to GCF_003992595.1_ASM399259v1_genomic.fna/dqc_result.json
[2024-01-25 20:00:02,846] [INFO] DFAST_QC completed!
[2024-01-25 20:00:02,846] [INFO] Total running time: 0h1m42s