[2024-01-24 13:25:58,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,121] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,121] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference
[2024-01-24 13:26:00,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,374] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,375] [INFO] Running command: gunzip -c /var/lib/cwl/stg1772760c-2adf-462f-8df5-a2bae281fd2f/GCF_009711465.1_ASM971146v1_genomic.fna.gz | prodigal -d GCF_009711465.1_ASM971146v1_genomic.fna/cds.fna -a GCF_009711465.1_ASM971146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:12,354] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:12,354] [INFO] Task started: HMMsearch
[2024-01-24 13:26:12,355] [INFO] Running command: hmmsearch --tblout GCF_009711465.1_ASM971146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference/reference_markers.hmm GCF_009711465.1_ASM971146v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:12,700] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:12,701] [INFO] Found 6/6 markers.
[2024-01-24 13:26:12,744] [INFO] Query marker FASTA was written to GCF_009711465.1_ASM971146v1_genomic.fna/markers.fasta
[2024-01-24 13:26:12,744] [INFO] Task started: Blastn
[2024-01-24 13:26:12,744] [INFO] Running command: blastn -query GCF_009711465.1_ASM971146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference/reference_markers.fasta -out GCF_009711465.1_ASM971146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:13,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:13,549] [INFO] Selected 23 target genomes.
[2024-01-24 13:26:13,549] [INFO] Target genome list was writen to GCF_009711465.1_ASM971146v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:13,568] [INFO] Task started: fastANI
[2024-01-24 13:26:13,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg1772760c-2adf-462f-8df5-a2bae281fd2f/GCF_009711465.1_ASM971146v1_genomic.fna.gz --refList GCF_009711465.1_ASM971146v1_genomic.fna/target_genomes.txt --output GCF_009711465.1_ASM971146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:33,305] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:33,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:33,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:33,322] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:33,322] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:33,323] [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
Sansalvadorimonas verongulae	strain=RKSG058	GCA_009711465.1	2172824	2172824	type	True	100.0	1330	1338	95	conclusive
Parendozoicomonas haliclonae		GCA_900174585.1	1960125	1960125	type	True	78.5311	320	1338	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	77.5042	108	1338	95	below_threshold
Kistimonas asteriae	strain=KMD 001	GCA_018263925.1	517724	517724	type	True	77.2176	123	1338	95	below_threshold
Endozoicomonas acroporae	strain=Acr-14	GCA_002864045.1	1701104	1701104	type	True	77.1055	108	1338	95	below_threshold
Endozoicomonas atrinae	strain=WP70	GCA_001647025.2	1333660	1333660	type	True	76.8652	93	1338	95	below_threshold
Oceanospirillum sanctuarii	strain=AK56	GCA_002150805.1	1434821	1434821	type	True	76.8173	55	1338	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000373945.1	305900	305900	type	True	76.7946	83	1338	95	below_threshold
Endozoicomonas ascidiicola	strain=AVMART05	GCA_001646945.1	1698521	1698521	type	True	76.776	93	1338	95	below_threshold
Endozoicomonas elysicola	strain=DSM 22380	GCA_000710775.1	305900	305900	type	True	76.7583	85	1338	95	below_threshold
Amphritea spongicola	strain=JCM 16668	GCA_017051665.1	707589	707589	type	True	76.6039	52	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:33,325] [INFO] DFAST Taxonomy check result was written to GCF_009711465.1_ASM971146v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:33,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:33,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:33,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference/checkm_data
[2024-01-24 13:26:33,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:33,379] [INFO] Task started: CheckM
[2024-01-24 13:26:33,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711465.1_ASM971146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711465.1_ASM971146v1_genomic.fna/checkm_input GCF_009711465.1_ASM971146v1_genomic.fna/checkm_result
[2024-01-24 13:27:13,233] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:13,235] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:13,262] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:13,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:13,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711465.1_ASM971146v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:13,264] [INFO] Task started: Blastn
[2024-01-24 13:27:13,264] [INFO] Running command: blastn -query GCF_009711465.1_ASM971146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1bd7079-ff29-4320-8955-13dc7fd88cea/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711465.1_ASM971146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:14,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:14,349] [INFO] Selected 26 target genomes.
[2024-01-24 13:27:14,349] [INFO] Target genome list was writen to GCF_009711465.1_ASM971146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:14,381] [INFO] Task started: fastANI
[2024-01-24 13:27:14,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg1772760c-2adf-462f-8df5-a2bae281fd2f/GCF_009711465.1_ASM971146v1_genomic.fna.gz --refList GCF_009711465.1_ASM971146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711465.1_ASM971146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:34,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:34,537] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:27:34,537] [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_900174585.1	s__Parendozoicomonas haliclonae	78.5252	320	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Parendozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583435.1	s__Endozoicomonas montiporae	77.4844	106	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.88	99.88	0.96	0.96	2	-
GCF_018263925.1	s__Kistimonas asteriae	77.1951	121	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002864045.1	s__Endozoicomonas acroporae	77.0931	108	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.93	98.92	0.89	0.89	3	-
GCF_009653635.1	s__Endozoicomonas sp009653635	77.0789	102	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744115.1	s__Endozoicomonas sp017744115	76.8857	95	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.21	98.21	0.89	0.89	2	-
GCF_001647025.1	s__Endozoicomonas atrinae	76.8356	91	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002150805.1	s__Oceanospirillum sanctuarii	76.8173	55	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Oceanospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710775.1	s__Endozoicomonas elysicola	76.7772	88	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900299555.1	s__Endozoicomonas sp900299555	76.7657	85	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002084115.1	s__Kistimonas sp002084115	76.7248	87	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Kistimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646945.1	s__Endozoicomonas ascidiicola	76.658	101	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Endozoicomonadaceae;g__Endozoicomonas	95.0	98.76	98.76	0.78	0.78	2	-
GCF_017051665.1	s__Amphritea spongicola	76.6059	52	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	76.2221	50	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	76.1892	51	1338	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:34,539] [INFO] GTDB search result was written to GCF_009711465.1_ASM971146v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:34,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:34,544] [INFO] DFAST_QC result json was written to GCF_009711465.1_ASM971146v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:34,544] [INFO] DFAST_QC completed!
[2024-01-24 13:27:34,544] [INFO] Total running time: 0h1m36s