[2024-01-24 14:23:02,300] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:02,303] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:02,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference
[2024-01-24 14:23:03,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:03,896] [INFO] Task started: Prodigal
[2024-01-24 14:23:03,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg31c8a4c5-ab09-4594-8928-03b23f2f684d/GCF_004104355.1_ASM410435v1_genomic.fna.gz | prodigal -d GCF_004104355.1_ASM410435v1_genomic.fna/cds.fna -a GCF_004104355.1_ASM410435v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:19,044] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:19,044] [INFO] Task started: HMMsearch
[2024-01-24 14:23:19,044] [INFO] Running command: hmmsearch --tblout GCF_004104355.1_ASM410435v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference/reference_markers.hmm GCF_004104355.1_ASM410435v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:19,560] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:19,561] [INFO] Found 6/6 markers.
[2024-01-24 14:23:19,616] [INFO] Query marker FASTA was written to GCF_004104355.1_ASM410435v1_genomic.fna/markers.fasta
[2024-01-24 14:23:19,617] [INFO] Task started: Blastn
[2024-01-24 14:23:19,617] [INFO] Running command: blastn -query GCF_004104355.1_ASM410435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference/reference_markers.fasta -out GCF_004104355.1_ASM410435v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:20,915] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:20,937] [INFO] Selected 17 target genomes.
[2024-01-24 14:23:20,937] [INFO] Target genome list was writen to GCF_004104355.1_ASM410435v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:20,959] [INFO] Task started: fastANI
[2024-01-24 14:23:20,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg31c8a4c5-ab09-4594-8928-03b23f2f684d/GCF_004104355.1_ASM410435v1_genomic.fna.gz --refList GCF_004104355.1_ASM410435v1_genomic.fna/target_genomes.txt --output GCF_004104355.1_ASM410435v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:43,164] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:43,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:43,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:43,256] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:43,256] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:43,256] [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
Photobacterium chitinilyticum	strain=BEI247	GCA_004104355.1	2485123	2485123	type	True	100.0	1894	1896	95	conclusive
Photobacterium alginatilyticum	strain=P03D4	GCA_009910675.1	1775171	1775171	type	True	83.7079	1361	1896	95	below_threshold
Photobacterium proteolyticum	strain=13-12	GCA_001939735.1	1903952	1903952	type	True	83.4553	1365	1896	95	below_threshold
Photobacterium marinum	strain=AK15	GCA_000331515.1	1056511	1056511	type	True	80.2814	766	1896	95	below_threshold
Photobacterium lipolyticum	strain=DSM 16190	GCA_003026475.1	266810	266810	type	True	80.1538	611	1896	95	below_threshold
Photobacterium sanctipauli	strain=A-394	GCA_000730475.1	1342794	1342794	type	True	80.025	414	1896	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	79.9939	423	1896	95	below_threshold
Photobacterium swingsii	strain=CECT 7576	GCA_024346715.1	680026	680026	type	True	79.727	447	1896	95	below_threshold
Photobacterium swingsii	strain=DSM 24669	GCA_003026435.1	680026	680026	type	True	79.5849	450	1896	95	below_threshold
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	79.5798	492	1896	95	below_threshold
Photobacterium swingsii	strain=CAIM 1393	GCA_001077885.1	680026	680026	type	True	79.5345	444	1896	95	below_threshold
Photobacterium jeanii	strain=R-40508	GCA_001650345.1	858640	858640	type	True	79.4743	441	1896	95	below_threshold
Photobacterium jeanii	strain=DSM 100339	GCA_003025495.1	858640	858640	type	True	79.407	454	1896	95	below_threshold
Photobacterium ganghwense	strain=JCM 12487	GCA_003025595.1	320778	320778	type	True	79.0266	477	1896	95	below_threshold
Vibrio natriegens	strain=14048	GCA_024508015.1	691	691	type	True	78.4908	156	1896	95	below_threshold
Vibrio chagasii	strain=LMG 21353	GCA_024347355.1	170679	170679	suspected-type	True	78.4533	160	1896	95	below_threshold
Vibrio furnissii	strain=PartQ-Vfurnissii-RM8376	GCA_022869905.1	29494	29494	type	True	77.6628	159	1896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:43,259] [INFO] DFAST Taxonomy check result was written to GCF_004104355.1_ASM410435v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:43,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:43,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:43,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference/checkm_data
[2024-01-24 14:23:43,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:43,343] [INFO] Task started: CheckM
[2024-01-24 14:23:43,344] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004104355.1_ASM410435v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004104355.1_ASM410435v1_genomic.fna/checkm_input GCF_004104355.1_ASM410435v1_genomic.fna/checkm_result
[2024-01-24 14:24:42,582] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:42,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.75%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:42,610] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:42,610] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:42,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004104355.1_ASM410435v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:42,611] [INFO] Task started: Blastn
[2024-01-24 14:24:42,611] [INFO] Running command: blastn -query GCF_004104355.1_ASM410435v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24daed52-3b10-45c2-9872-f69f908687a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004104355.1_ASM410435v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:46,342] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:46,346] [INFO] Selected 14 target genomes.
[2024-01-24 14:24:46,346] [INFO] Target genome list was writen to GCF_004104355.1_ASM410435v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:46,359] [INFO] Task started: fastANI
[2024-01-24 14:24:46,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg31c8a4c5-ab09-4594-8928-03b23f2f684d/GCF_004104355.1_ASM410435v1_genomic.fna.gz --refList GCF_004104355.1_ASM410435v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004104355.1_ASM410435v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:02,989] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:03,061] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:03,062] [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_004104355.1	s__Photobacterium chitinilyticum	100.0	1894	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009910675.1	s__Photobacterium alginatilyticum	83.7182	1360	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001939735.1	s__Photobacterium proteolyticum	83.4553	1365	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331515.1	s__Photobacterium marinum	80.278	766	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	96.66	96.66	0.88	0.88	2	-
GCF_003026475.1	s__Photobacterium lipolyticum	80.1334	616	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002265265.1	s__Photobacterium sanguinicancri	79.8698	395	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.87	97.87	0.90	0.90	2	-
GCF_003026495.1	s__Photobacterium sanctipauli	79.859	565	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026215.1	s__Photobacterium indicum	79.5798	492	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001077885.1	s__Photobacterium swingsii	79.548	445	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001650345.1	s__Photobacterium jeanii	79.4774	442	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001029435.1	s__Photobacterium aphoticum	79.4612	469	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.09	97.29	0.97	0.93	4	-
GCF_003026285.1	s__Photobacterium profundum	79.4121	496	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000196255.1	s__Photobacterium profundum_A	79.1096	496	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_003025595.1	s__Photobacterium ganghwense	79.0405	475	1896	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.50	98.82	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:03,063] [INFO] GTDB search result was written to GCF_004104355.1_ASM410435v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:03,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:03,068] [INFO] DFAST_QC result json was written to GCF_004104355.1_ASM410435v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:03,068] [INFO] DFAST_QC completed!
[2024-01-24 14:25:03,068] [INFO] Total running time: 0h2m1s