[2024-01-25 20:26:05,729] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:05,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:05,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference
[2024-01-25 20:26:06,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:06,925] [INFO] Task started: Prodigal
[2024-01-25 20:26:06,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg610d8fe6-ea1e-4998-9fef-c6a8fa2415e1/GCF_000948975.2_ASM94897v2_genomic.fna.gz | prodigal -d GCF_000948975.2_ASM94897v2_genomic.fna/cds.fna -a GCF_000948975.2_ASM94897v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:28,197] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:28,197] [INFO] Task started: HMMsearch
[2024-01-25 20:26:28,197] [INFO] Running command: hmmsearch --tblout GCF_000948975.2_ASM94897v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference/reference_markers.hmm GCF_000948975.2_ASM94897v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:28,477] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:28,478] [INFO] Found 6/6 markers.
[2024-01-25 20:26:28,532] [INFO] Query marker FASTA was written to GCF_000948975.2_ASM94897v2_genomic.fna/markers.fasta
[2024-01-25 20:26:28,533] [INFO] Task started: Blastn
[2024-01-25 20:26:28,533] [INFO] Running command: blastn -query GCF_000948975.2_ASM94897v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference/reference_markers.fasta -out GCF_000948975.2_ASM94897v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:29,229] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:29,232] [INFO] Selected 23 target genomes.
[2024-01-25 20:26:29,232] [INFO] Target genome list was writen to GCF_000948975.2_ASM94897v2_genomic.fna/target_genomes.txt
[2024-01-25 20:26:29,254] [INFO] Task started: fastANI
[2024-01-25 20:26:29,254] [INFO] Running command: fastANI --query /var/lib/cwl/stg610d8fe6-ea1e-4998-9fef-c6a8fa2415e1/GCF_000948975.2_ASM94897v2_genomic.fna.gz --refList GCF_000948975.2_ASM94897v2_genomic.fna/target_genomes.txt --output GCF_000948975.2_ASM94897v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:26:47,661] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:47,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:26:47,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:26:47,672] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:26:47,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:26:47,672] [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
Thalassomonas actiniarum	strain=A5K-106	GCA_000948975.1	485447	485447	type	True	99.971	2399	2497	95	conclusive
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	84.211	1682	2497	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	79.3392	152	2497	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.3406	103	2497	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.0684	101	2497	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.0426	98	2497	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.9837	97	2497	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.9534	137	2497	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.7185	133	2497	95	below_threshold
Thalassotalea mangrovi	strain=ZS-4	GCA_005116735.1	2572245	2572245	type	True	77.5969	126	2497	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	77.5776	164	2497	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	77.5574	173	2497	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	76.1864	72	2497	95	below_threshold
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	75.9	69	2497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:26:47,674] [INFO] DFAST Taxonomy check result was written to GCF_000948975.2_ASM94897v2_genomic.fna/tc_result.tsv
[2024-01-25 20:26:47,674] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:26:47,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:26:47,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference/checkm_data
[2024-01-25 20:26:47,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:26:47,747] [INFO] Task started: CheckM
[2024-01-25 20:26:47,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000948975.2_ASM94897v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000948975.2_ASM94897v2_genomic.fna/checkm_input GCF_000948975.2_ASM94897v2_genomic.fna/checkm_result
[2024-01-25 20:27:48,769] [INFO] Task succeeded: CheckM
[2024-01-25 20:27:48,770] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:27:48,804] [INFO] ===== Completeness check finished =====
[2024-01-25 20:27:48,805] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:27:48,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000948975.2_ASM94897v2_genomic.fna/markers.fasta)
[2024-01-25 20:27:48,806] [INFO] Task started: Blastn
[2024-01-25 20:27:48,806] [INFO] Running command: blastn -query GCF_000948975.2_ASM94897v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f06d94a-f974-451c-8420-cf30df57dad8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000948975.2_ASM94897v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:49,997] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:50,000] [INFO] Selected 20 target genomes.
[2024-01-25 20:27:50,000] [INFO] Target genome list was writen to GCF_000948975.2_ASM94897v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:27:50,014] [INFO] Task started: fastANI
[2024-01-25 20:27:50,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg610d8fe6-ea1e-4998-9fef-c6a8fa2415e1/GCF_000948975.2_ASM94897v2_genomic.fna.gz --refList GCF_000948975.2_ASM94897v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000948975.2_ASM94897v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:07,570] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:07,583] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:07,583] [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_000948975.1	s__Thalassomonas actiniarum	99.971	2399	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000948985.1	s__Thalassomonas viridans	84.2162	1680	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	79.52	119	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004752005.1	s__Thalassotalea_A sp004752005	79.3092	90	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	95.63	95.63	0.92	0.92	2	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	79.1052	128	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	78.9676	153	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	78.8582	149	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003545765.1	s__Litorilituus sp003545765	78.8484	96	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014898095.1	s__Thalassotalea sp014898095	78.7355	141	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.2489	98	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	78.2103	112	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	78.1228	134	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	78.1049	100	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	78.0201	96	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104475.1	s__Cognaticolwellia mytili	77.9534	137	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744155.1	s__Thalassotalea sp017744155	77.9391	146	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.6984	142	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005116735.1	s__Thalassotalea_A mangrovi	77.617	125	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215385.1	s__Colwellia_A sp013215385	77.4438	137	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401725.1	s__GCA-2401725 sp002401725	77.0402	102	2497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:07,584] [INFO] GTDB search result was written to GCF_000948975.2_ASM94897v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:07,585] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:07,595] [INFO] DFAST_QC result json was written to GCF_000948975.2_ASM94897v2_genomic.fna/dqc_result.json
[2024-01-25 20:28:07,595] [INFO] DFAST_QC completed!
[2024-01-25 20:28:07,595] [INFO] Total running time: 0h2m2s