[2024-01-24 12:42:09,081] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:09,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:09,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference
[2024-01-24 12:42:10,405] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:10,406] [INFO] Task started: Prodigal
[2024-01-24 12:42:10,406] [INFO] Running command: gunzip -c /var/lib/cwl/stgc403ece6-0322-4cc1-a1f7-ed1a059a65e2/GCF_006459125.1_ASM645912v1_genomic.fna.gz | prodigal -d GCF_006459125.1_ASM645912v1_genomic.fna/cds.fna -a GCF_006459125.1_ASM645912v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:15,638] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:15,638] [INFO] Task started: HMMsearch
[2024-01-24 12:42:15,638] [INFO] Running command: hmmsearch --tblout GCF_006459125.1_ASM645912v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference/reference_markers.hmm GCF_006459125.1_ASM645912v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:15,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:15,947] [INFO] Found 6/6 markers.
[2024-01-24 12:42:15,974] [INFO] Query marker FASTA was written to GCF_006459125.1_ASM645912v1_genomic.fna/markers.fasta
[2024-01-24 12:42:15,974] [INFO] Task started: Blastn
[2024-01-24 12:42:15,975] [INFO] Running command: blastn -query GCF_006459125.1_ASM645912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference/reference_markers.fasta -out GCF_006459125.1_ASM645912v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:16,575] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:16,578] [INFO] Selected 11 target genomes.
[2024-01-24 12:42:16,579] [INFO] Target genome list was writen to GCF_006459125.1_ASM645912v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:16,592] [INFO] Task started: fastANI
[2024-01-24 12:42:16,592] [INFO] Running command: fastANI --query /var/lib/cwl/stgc403ece6-0322-4cc1-a1f7-ed1a059a65e2/GCF_006459125.1_ASM645912v1_genomic.fna.gz --refList GCF_006459125.1_ASM645912v1_genomic.fna/target_genomes.txt --output GCF_006459125.1_ASM645912v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:22,941] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:22,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:22,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:22,952] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:22,952] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:22,952] [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
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	100.0	1001	1005	95	conclusive
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	99.9857	970	1005	95	conclusive
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	80.4113	601	1005	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	80.2514	593	1005	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	79.3676	405	1005	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	79.1149	392	1005	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	79.0215	434	1005	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	78.7952	356	1005	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	78.0187	227	1005	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	77.9138	297	1005	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	77.8741	374	1005	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:22,954] [INFO] DFAST Taxonomy check result was written to GCF_006459125.1_ASM645912v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:22,955] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:22,955] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:22,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference/checkm_data
[2024-01-24 12:42:22,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:22,988] [INFO] Task started: CheckM
[2024-01-24 12:42:22,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006459125.1_ASM645912v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006459125.1_ASM645912v1_genomic.fna/checkm_input GCF_006459125.1_ASM645912v1_genomic.fna/checkm_result
[2024-01-24 12:42:45,347] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:45,349] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:45,370] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:45,371] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:45,371] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006459125.1_ASM645912v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:45,372] [INFO] Task started: Blastn
[2024-01-24 12:42:45,372] [INFO] Running command: blastn -query GCF_006459125.1_ASM645912v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg720093f3-5521-4d1b-a573-c968608db754/dqc_reference/reference_markers_gtdb.fasta -out GCF_006459125.1_ASM645912v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:46,236] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:46,242] [INFO] Selected 16 target genomes.
[2024-01-24 12:42:46,242] [INFO] Target genome list was writen to GCF_006459125.1_ASM645912v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:46,352] [INFO] Task started: fastANI
[2024-01-24 12:42:46,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgc403ece6-0322-4cc1-a1f7-ed1a059a65e2/GCF_006459125.1_ASM645912v1_genomic.fna.gz --refList GCF_006459125.1_ASM645912v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006459125.1_ASM645912v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:55,520] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:55,537] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:55,538] [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_006459125.1	s__Halarcobacter anaerophilus	100.0	1000	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.86	97.73	0.95	0.89	3	conclusive
GCF_013201825.1	s__Halarcobacter ebronensis	80.3799	602	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCF_003346815.1	s__Halarcobacter bivalviorum	79.3617	406	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_004116625.1	s__Halarcobacter mediterraneus	79.21	438	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252105.1	s__Halarcobacter sp003252105	79.193	420	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771535.1	s__Halarcobacter arenosus	79.0266	433	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	78.9556	424	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	78.905	366	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544935.1	s__Malaciobacter molluscorum	78.8168	359	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCA_004116455.1	s__Halarcobacter sp004116455	78.7877	376	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCA_004118855.1	s__Halarcobacter sp004118855	78.771	401	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	78.6291	445	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116725.1	s__Malaciobacter sp004116725	78.4111	359	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	78.3363	341	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_013201725.1	s__Aliarcobacter defluvii	78.1427	376	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_004299785.2	s__Aliarcobacter porcinus	77.9936	222	1005	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:55,539] [INFO] GTDB search result was written to GCF_006459125.1_ASM645912v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:55,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:55,544] [INFO] DFAST_QC result json was written to GCF_006459125.1_ASM645912v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:55,545] [INFO] DFAST_QC completed!
[2024-01-24 12:42:55,545] [INFO] Total running time: 0h0m46s