[2024-01-24 14:55:08,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference
[2024-01-24 14:55:10,134] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,135] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e5d67a4-acbb-47c4-be33-f3a8762131c6/GCF_005938655.1_ASM593865v1_genomic.fna.gz | prodigal -d GCF_005938655.1_ASM593865v1_genomic.fna/cds.fna -a GCF_005938655.1_ASM593865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:23,069] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:23,070] [INFO] Task started: HMMsearch
[2024-01-24 14:55:23,070] [INFO] Running command: hmmsearch --tblout GCF_005938655.1_ASM593865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference/reference_markers.hmm GCF_005938655.1_ASM593865v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:23,340] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:23,342] [INFO] Found 6/6 markers.
[2024-01-24 14:55:23,385] [INFO] Query marker FASTA was written to GCF_005938655.1_ASM593865v1_genomic.fna/markers.fasta
[2024-01-24 14:55:23,386] [INFO] Task started: Blastn
[2024-01-24 14:55:23,386] [INFO] Running command: blastn -query GCF_005938655.1_ASM593865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference/reference_markers.fasta -out GCF_005938655.1_ASM593865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:24,353] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:24,356] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:24,356] [INFO] Target genome list was writen to GCF_005938655.1_ASM593865v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:24,361] [INFO] Task started: fastANI
[2024-01-24 14:55:24,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e5d67a4-acbb-47c4-be33-f3a8762131c6/GCF_005938655.1_ASM593865v1_genomic.fna.gz --refList GCF_005938655.1_ASM593865v1_genomic.fna/target_genomes.txt --output GCF_005938655.1_ASM593865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:34,869] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:34,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:34,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:34,879] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:34,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:34,880] [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 gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	100.0	1379	1380	95	conclusive
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	90.3306	1012	1380	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	87.9949	1046	1380	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	85.0442	878	1380	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	82.4502	842	1380	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	80.4902	730	1380	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.4115	583	1380	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	80.3996	712	1380	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	78.0849	311	1380	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.5647	298	1380	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.4378	309	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:34,881] [INFO] DFAST Taxonomy check result was written to GCF_005938655.1_ASM593865v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:34,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:34,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:34,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference/checkm_data
[2024-01-24 14:55:34,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:34,928] [INFO] Task started: CheckM
[2024-01-24 14:55:34,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005938655.1_ASM593865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005938655.1_ASM593865v1_genomic.fna/checkm_input GCF_005938655.1_ASM593865v1_genomic.fna/checkm_result
[2024-01-24 14:56:15,885] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:15,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:15,903] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:15,903] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:15,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005938655.1_ASM593865v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:15,904] [INFO] Task started: Blastn
[2024-01-24 14:56:15,904] [INFO] Running command: blastn -query GCF_005938655.1_ASM593865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16b53d9e-3ae2-45b5-923a-bdbd75c12a55/dqc_reference/reference_markers_gtdb.fasta -out GCF_005938655.1_ASM593865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:17,705] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:17,709] [INFO] Selected 7 target genomes.
[2024-01-24 14:56:17,709] [INFO] Target genome list was writen to GCF_005938655.1_ASM593865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:17,717] [INFO] Task started: fastANI
[2024-01-24 14:56:17,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e5d67a4-acbb-47c4-be33-f3a8762131c6/GCF_005938655.1_ASM593865v1_genomic.fna.gz --refList GCF_005938655.1_ASM593865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005938655.1_ASM593865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:25,342] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:25,352] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:25,352] [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_005938655.1	s__Alcanivorax gelatiniphagus	100.0	1379	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	conclusive
GCF_016906305.1	s__Alcanivorax marinus_B	90.4046	1129	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	87.9858	1047	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_016785095.1	s__Alcanivorax marinus_A	86.7807	1062	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	85.0411	878	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCA_017794945.1	s__Alcanivorax sp009711585	84.7207	797	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_004360225.1	s__Alcanivorax sp004360225	80.3803	695	1380	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:25,354] [INFO] GTDB search result was written to GCF_005938655.1_ASM593865v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:25,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:25,359] [INFO] DFAST_QC result json was written to GCF_005938655.1_ASM593865v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:25,359] [INFO] DFAST_QC completed!
[2024-01-24 14:56:25,359] [INFO] Total running time: 0h1m17s