[2024-01-25 18:57:20,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:20,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:20,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference
[2024-01-25 18:57:21,801] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:21,802] [INFO] Task started: Prodigal
[2024-01-25 18:57:21,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f5c9d47-a5c9-4181-be86-1b8128ac98e4/GCF_015356855.1_ASM1535685v1_genomic.fna.gz | prodigal -d GCF_015356855.1_ASM1535685v1_genomic.fna/cds.fna -a GCF_015356855.1_ASM1535685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:31,003] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:31,003] [INFO] Task started: HMMsearch
[2024-01-25 18:57:31,003] [INFO] Running command: hmmsearch --tblout GCF_015356855.1_ASM1535685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference/reference_markers.hmm GCF_015356855.1_ASM1535685v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:31,232] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:31,233] [INFO] Found 6/6 markers.
[2024-01-25 18:57:31,262] [INFO] Query marker FASTA was written to GCF_015356855.1_ASM1535685v1_genomic.fna/markers.fasta
[2024-01-25 18:57:31,262] [INFO] Task started: Blastn
[2024-01-25 18:57:31,262] [INFO] Running command: blastn -query GCF_015356855.1_ASM1535685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference/reference_markers.fasta -out GCF_015356855.1_ASM1535685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:32,115] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:32,118] [INFO] Selected 9 target genomes.
[2024-01-25 18:57:32,118] [INFO] Target genome list was writen to GCF_015356855.1_ASM1535685v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:32,124] [INFO] Task started: fastANI
[2024-01-25 18:57:32,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5c9d47-a5c9-4181-be86-1b8128ac98e4/GCF_015356855.1_ASM1535685v1_genomic.fna.gz --refList GCF_015356855.1_ASM1535685v1_genomic.fna/target_genomes.txt --output GCF_015356855.1_ASM1535685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:40,463] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:40,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:40,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:40,470] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:40,471] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:40,471] [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
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	100.0	1135	1141	95	conclusive
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	85.5196	909	1141	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	85.0283	863	1141	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	84.9872	810	1141	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	82.5642	774	1141	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	80.485	645	1141	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	78.2167	314	1141	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.8157	264	1141	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.6519	121	1141	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:40,472] [INFO] DFAST Taxonomy check result was written to GCF_015356855.1_ASM1535685v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:40,473] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:40,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:40,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference/checkm_data
[2024-01-25 18:57:40,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:40,511] [INFO] Task started: CheckM
[2024-01-25 18:57:40,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015356855.1_ASM1535685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015356855.1_ASM1535685v1_genomic.fna/checkm_input GCF_015356855.1_ASM1535685v1_genomic.fna/checkm_result
[2024-01-25 18:58:09,496] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:09,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:09,514] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:09,514] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:09,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015356855.1_ASM1535685v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:09,515] [INFO] Task started: Blastn
[2024-01-25 18:58:09,515] [INFO] Running command: blastn -query GCF_015356855.1_ASM1535685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg175adc3e-89a1-494c-91aa-ca9de23e871b/dqc_reference/reference_markers_gtdb.fasta -out GCF_015356855.1_ASM1535685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:11,149] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:11,153] [INFO] Selected 8 target genomes.
[2024-01-25 18:58:11,153] [INFO] Target genome list was writen to GCF_015356855.1_ASM1535685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:11,163] [INFO] Task started: fastANI
[2024-01-25 18:58:11,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5c9d47-a5c9-4181-be86-1b8128ac98e4/GCF_015356855.1_ASM1535685v1_genomic.fna.gz --refList GCF_015356855.1_ASM1535685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015356855.1_ASM1535685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:18,735] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:18,741] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:18,741] [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_015356855.1	s__Alcanivorax venustensis	100.0	1135	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	conclusive
GCA_017794945.1	s__Alcanivorax sp009711585	94.8142	916	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCA_002389055.1	s__Alcanivorax sp002389055	92.994	850	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCF_015265435.1	s__Alcanivorax profundimaris	85.5275	908	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_016906305.1	s__Alcanivorax marinus_B	85.0617	868	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	85.0164	864	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_016785095.1	s__Alcanivorax marinus_A	83.8394	819	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402545.1	s__Saccharospirillum sp018402545	78.2891	72	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:18,743] [INFO] GTDB search result was written to GCF_015356855.1_ASM1535685v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:18,743] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:18,746] [INFO] DFAST_QC result json was written to GCF_015356855.1_ASM1535685v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:18,746] [INFO] DFAST_QC completed!
[2024-01-25 18:58:18,746] [INFO] Total running time: 0h0m58s