[2024-01-24 14:38:45,579] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference
[2024-01-24 14:38:48,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,274] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a22282f-fd4e-40b6-93ba-bab3479b79d1/GCF_003346815.1_ASM334681v1_genomic.fna.gz | prodigal -d GCF_003346815.1_ASM334681v1_genomic.fna/cds.fna -a GCF_003346815.1_ASM334681v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:52,330] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:52,330] [INFO] Task started: HMMsearch
[2024-01-24 14:38:52,330] [INFO] Running command: hmmsearch --tblout GCF_003346815.1_ASM334681v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference/reference_markers.hmm GCF_003346815.1_ASM334681v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:52,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:52,583] [INFO] Found 6/6 markers.
[2024-01-24 14:38:52,612] [INFO] Query marker FASTA was written to GCF_003346815.1_ASM334681v1_genomic.fna/markers.fasta
[2024-01-24 14:38:52,613] [INFO] Task started: Blastn
[2024-01-24 14:38:52,613] [INFO] Running command: blastn -query GCF_003346815.1_ASM334681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference/reference_markers.fasta -out GCF_003346815.1_ASM334681v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:55,166] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:55,171] [INFO] Selected 16 target genomes.
[2024-01-24 14:38:55,171] [INFO] Target genome list was writen to GCF_003346815.1_ASM334681v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:55,321] [INFO] Task started: fastANI
[2024-01-24 14:38:55,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a22282f-fd4e-40b6-93ba-bab3479b79d1/GCF_003346815.1_ASM334681v1_genomic.fna.gz --refList GCF_003346815.1_ASM334681v1_genomic.fna/target_genomes.txt --output GCF_003346815.1_ASM334681v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:05,003] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:05,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:05,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:05,019] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:05,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:05,019] [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 bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	100.0	892	894	95	conclusive
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	99.9857	877	894	95	conclusive
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	80.5974	491	894	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	80.3278	515	894	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	80.2073	421	894	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	80.1505	502	894	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	80.1222	454	894	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	80.1025	471	894	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	80.0293	402	894	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	79.9377	470	894	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.8829	415	894	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	79.6983	413	894	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.5513	423	894	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	79.2413	410	894	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	79.171	389	894	95	below_threshold
Arcobacter nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	79.1686	413	894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:05,021] [INFO] DFAST Taxonomy check result was written to GCF_003346815.1_ASM334681v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:05,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:05,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:05,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference/checkm_data
[2024-01-24 14:39:05,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:05,056] [INFO] Task started: CheckM
[2024-01-24 14:39:05,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003346815.1_ASM334681v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003346815.1_ASM334681v1_genomic.fna/checkm_input GCF_003346815.1_ASM334681v1_genomic.fna/checkm_result
[2024-01-24 14:39:25,998] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:26,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:26,024] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:26,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:26,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003346815.1_ASM334681v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:26,025] [INFO] Task started: Blastn
[2024-01-24 14:39:26,025] [INFO] Running command: blastn -query GCF_003346815.1_ASM334681v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69e53a6a-430d-46a0-b73a-62e1d5393b7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003346815.1_ASM334681v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:26,869] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:26,872] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:26,872] [INFO] Target genome list was writen to GCF_003346815.1_ASM334681v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:26,879] [INFO] Task started: fastANI
[2024-01-24 14:39:26,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a22282f-fd4e-40b6-93ba-bab3479b79d1/GCF_003346815.1_ASM334681v1_genomic.fna.gz --refList GCF_003346815.1_ASM334681v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003346815.1_ASM334681v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:32,901] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:32,909] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:32,909] [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_003346815.1	s__Halarcobacter bivalviorum	100.0	892	894	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	conclusive
GCA_004116455.1	s__Halarcobacter sp004116455	86.3846	722	894	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	85.4065	686	894	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	85.2392	700	894	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004116625.1	s__Halarcobacter mediterraneus	83.0612	596	894	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	80.6615	486	894	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	80.3426	438	894	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346775.1	s__Malaciobacter mytili	80.3167	517	894	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:32,911] [INFO] GTDB search result was written to GCF_003346815.1_ASM334681v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:32,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:32,915] [INFO] DFAST_QC result json was written to GCF_003346815.1_ASM334681v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:32,915] [INFO] DFAST_QC completed!
[2024-01-24 14:39:32,915] [INFO] Total running time: 0h0m47s