[2024-01-24 10:57:26,773] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:26,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:26,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference
[2024-01-24 10:57:28,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:28,141] [INFO] Task started: Prodigal
[2024-01-24 10:57:28,141] [INFO] Running command: gunzip -c /var/lib/cwl/stg35c38d4b-85a0-4b2d-8793-5b0fd5b35ded/GCF_005117025.1_ASM511702v1_genomic.fna.gz | prodigal -d GCF_005117025.1_ASM511702v1_genomic.fna/cds.fna -a GCF_005117025.1_ASM511702v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:38,547] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:38,547] [INFO] Task started: HMMsearch
[2024-01-24 10:57:38,547] [INFO] Running command: hmmsearch --tblout GCF_005117025.1_ASM511702v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference/reference_markers.hmm GCF_005117025.1_ASM511702v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:38,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:38,900] [INFO] Found 6/6 markers.
[2024-01-24 10:57:38,942] [INFO] Query marker FASTA was written to GCF_005117025.1_ASM511702v1_genomic.fna/markers.fasta
[2024-01-24 10:57:38,942] [INFO] Task started: Blastn
[2024-01-24 10:57:38,942] [INFO] Running command: blastn -query GCF_005117025.1_ASM511702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference/reference_markers.fasta -out GCF_005117025.1_ASM511702v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:39,720] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:39,727] [INFO] Selected 11 target genomes.
[2024-01-24 10:57:39,728] [INFO] Target genome list was writen to GCF_005117025.1_ASM511702v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:39,766] [INFO] Task started: fastANI
[2024-01-24 10:57:39,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c38d4b-85a0-4b2d-8793-5b0fd5b35ded/GCF_005117025.1_ASM511702v1_genomic.fna.gz --refList GCF_005117025.1_ASM511702v1_genomic.fna/target_genomes.txt --output GCF_005117025.1_ASM511702v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:49,193] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:49,193] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:49,194] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:49,200] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:49,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:49,201] [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
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	100.0	1498	1498	95	conclusive
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	88.4303	1132	1498	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	86.5515	1067	1498	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	83.224	903	1498	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	83.1351	931	1498	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.119	435	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:49,202] [INFO] DFAST Taxonomy check result was written to GCF_005117025.1_ASM511702v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:49,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:49,203] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:49,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference/checkm_data
[2024-01-24 10:57:49,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:49,246] [INFO] Task started: CheckM
[2024-01-24 10:57:49,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005117025.1_ASM511702v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005117025.1_ASM511702v1_genomic.fna/checkm_input GCF_005117025.1_ASM511702v1_genomic.fna/checkm_result
[2024-01-24 10:58:23,712] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:23,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:23,726] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:23,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:23,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005117025.1_ASM511702v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:23,727] [INFO] Task started: Blastn
[2024-01-24 10:58:23,727] [INFO] Running command: blastn -query GCF_005117025.1_ASM511702v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a339f4a-4964-4259-8c55-9e542682810f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005117025.1_ASM511702v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:24,848] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:24,852] [INFO] Selected 9 target genomes.
[2024-01-24 10:58:24,852] [INFO] Target genome list was writen to GCF_005117025.1_ASM511702v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:24,858] [INFO] Task started: fastANI
[2024-01-24 10:58:24,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg35c38d4b-85a0-4b2d-8793-5b0fd5b35ded/GCF_005117025.1_ASM511702v1_genomic.fna.gz --refList GCF_005117025.1_ASM511702v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005117025.1_ASM511702v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:34,637] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:34,646] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:34,646] [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_005117025.1	s__Alteromonas portus	100.0	1498	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000808575.1	s__Alteromonas marina	89.285	1132	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_000172635.2	s__Alteromonas macleodii	88.4303	1132	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_903772925.1	s__Alteromonas macleodii_A	87.3003	1207	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885075.1	s__Alteromonas sp001885075	86.8163	860	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	86.5515	1067	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_003443615.1	s__Alteromonas sp003443615	85.8906	1185	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000597705.1	s__Alteromonas sp000597705	85.177	1143	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_000020585.3	s__Alteromonas mediterranea	83.224	903	1498	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:34,648] [INFO] GTDB search result was written to GCF_005117025.1_ASM511702v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:34,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:34,654] [INFO] DFAST_QC result json was written to GCF_005117025.1_ASM511702v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:34,654] [INFO] DFAST_QC completed!
[2024-01-24 10:58:34,654] [INFO] Total running time: 0h1m8s