[2023-06-29 11:07:33,343] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:07:33,345] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:07:33,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference
[2023-06-29 11:07:35,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:07:35,766] [INFO] Task started: Prodigal
[2023-06-29 11:07:35,767] [INFO] Running command: gunzip -c /var/lib/cwl/stgacab0a4b-fd8b-405e-a7de-f186086632a2/GCA_020049165.1_ASM2004916v1_genomic.fna.gz | prodigal -d GCA_020049165.1_ASM2004916v1_genomic.fna/cds.fna -a GCA_020049165.1_ASM2004916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:07:46,482] [INFO] Task succeeded: Prodigal
[2023-06-29 11:07:46,483] [INFO] Task started: HMMsearch
[2023-06-29 11:07:46,483] [INFO] Running command: hmmsearch --tblout GCA_020049165.1_ASM2004916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference/reference_markers.hmm GCA_020049165.1_ASM2004916v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:07:46,707] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:07:46,709] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgacab0a4b-fd8b-405e-a7de-f186086632a2/GCA_020049165.1_ASM2004916v1_genomic.fna.gz]
[2023-06-29 11:07:46,734] [INFO] Query marker FASTA was written to GCA_020049165.1_ASM2004916v1_genomic.fna/markers.fasta
[2023-06-29 11:07:46,735] [INFO] Task started: Blastn
[2023-06-29 11:07:46,735] [INFO] Running command: blastn -query GCA_020049165.1_ASM2004916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference/reference_markers.fasta -out GCA_020049165.1_ASM2004916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:07:47,317] [INFO] Task succeeded: Blastn
[2023-06-29 11:07:47,321] [INFO] Selected 14 target genomes.
[2023-06-29 11:07:47,322] [INFO] Target genome list was writen to GCA_020049165.1_ASM2004916v1_genomic.fna/target_genomes.txt
[2023-06-29 11:07:47,324] [INFO] Task started: fastANI
[2023-06-29 11:07:47,324] [INFO] Running command: fastANI --query /var/lib/cwl/stgacab0a4b-fd8b-405e-a7de-f186086632a2/GCA_020049165.1_ASM2004916v1_genomic.fna.gz --refList GCA_020049165.1_ASM2004916v1_genomic.fna/target_genomes.txt --output GCA_020049165.1_ASM2004916v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:07:58,112] [INFO] Task succeeded: fastANI
[2023-06-29 11:07:58,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:07:58,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:07:58,127] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:07:58,127] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:07:58,127] [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
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	76.8874	84	726	95	below_threshold
Maribellus comscasis	strain=WC007	GCA_009762775.1	2681766	2681766	type	True	76.6363	86	726	95	below_threshold
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	76.5428	77	726	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	76.5304	69	726	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.4988	66	726	95	below_threshold
Draconibacterium mangrovi	strain=GM2-18	GCA_010586825.1	2697469	2697469	type	True	76.4848	76	726	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	76.4743	71	726	95	below_threshold
Draconibacterium halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	76.2403	76	726	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:07:58,129] [INFO] DFAST Taxonomy check result was written to GCA_020049165.1_ASM2004916v1_genomic.fna/tc_result.tsv
[2023-06-29 11:07:58,130] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:07:58,130] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:07:58,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference/checkm_data
[2023-06-29 11:07:58,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:07:58,164] [INFO] Task started: CheckM
[2023-06-29 11:07:58,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020049165.1_ASM2004916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020049165.1_ASM2004916v1_genomic.fna/checkm_input GCA_020049165.1_ASM2004916v1_genomic.fna/checkm_result
[2023-06-29 11:08:33,632] [INFO] Task succeeded: CheckM
[2023-06-29 11:08:33,633] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:08:33,652] [INFO] ===== Completeness check finished =====
[2023-06-29 11:08:33,652] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:08:33,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020049165.1_ASM2004916v1_genomic.fna/markers.fasta)
[2023-06-29 11:08:33,653] [INFO] Task started: Blastn
[2023-06-29 11:08:33,653] [INFO] Running command: blastn -query GCA_020049165.1_ASM2004916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75d41966-d154-46a3-b457-83d389c4673e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020049165.1_ASM2004916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:08:34,395] [INFO] Task succeeded: Blastn
[2023-06-29 11:08:34,399] [INFO] Selected 15 target genomes.
[2023-06-29 11:08:34,400] [INFO] Target genome list was writen to GCA_020049165.1_ASM2004916v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:08:34,403] [INFO] Task started: fastANI
[2023-06-29 11:08:34,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgacab0a4b-fd8b-405e-a7de-f186086632a2/GCA_020049165.1_ASM2004916v1_genomic.fna.gz --refList GCA_020049165.1_ASM2004916v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020049165.1_ASM2004916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:08:45,369] [INFO] Task succeeded: fastANI
[2023-06-29 11:08:45,383] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 11:08:45,383] [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
GCA_009773765.1	s__Draconibacterium sp009773765	80.5317	323	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705335.1	s__Draconibacterium sp016705335	79.0403	239	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493625.1	s__Draconibacterium sp015493625	77.2018	59	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203755.1	s__Draconibacterium sp013203755	77.0361	83	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620585.1	s__Draconibacterium sp011620585	76.7665	62	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762775.1	s__Draconibacterium comscasis	76.6363	86	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949475.1	s__Draconibacterium sediminis	76.5428	77	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010586825.1	s__Draconibacterium mangrovi	76.4848	76	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648265.1	s__Draconibacterium sp018648265	76.4418	119	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.94	99.92	0.96	0.95	4	-
GCA_016931875.1	s__Draconibacterium sp016931875	76.2988	64	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010448835.1	s__Draconibacterium halophilum	76.2608	75	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506435.1	s__GWE2-42-39 sp003506435	76.063	52	726	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__GWE2-42-39	95.0	99.97	99.92	0.99	0.98	6	-
--------------------------------------------------------------------------------
[2023-06-29 11:08:45,385] [INFO] GTDB search result was written to GCA_020049165.1_ASM2004916v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:08:45,386] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:08:45,389] [INFO] DFAST_QC result json was written to GCA_020049165.1_ASM2004916v1_genomic.fna/dqc_result.json
[2023-06-29 11:08:45,390] [INFO] DFAST_QC completed!
[2023-06-29 11:08:45,390] [INFO] Total running time: 0h1m12s