[2024-01-25 20:04:35,666] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:35,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:35,671] [INFO] DQC Reference Directory: /var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference
[2024-01-25 20:04:36,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:36,798] [INFO] Task started: Prodigal
[2024-01-25 20:04:36,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg49a2215e-fa68-4b45-b9a8-de87e57b8748/GCF_003014695.1_ASM301469v1_genomic.fna.gz | prodigal -d GCF_003014695.1_ASM301469v1_genomic.fna/cds.fna -a GCF_003014695.1_ASM301469v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:14,643] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:14,643] [INFO] Task started: HMMsearch
[2024-01-25 20:05:14,643] [INFO] Running command: hmmsearch --tblout GCF_003014695.1_ASM301469v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference/reference_markers.hmm GCF_003014695.1_ASM301469v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:14,943] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:14,944] [INFO] Found 6/6 markers.
[2024-01-25 20:05:15,007] [INFO] Query marker FASTA was written to GCF_003014695.1_ASM301469v1_genomic.fna/markers.fasta
[2024-01-25 20:05:15,007] [INFO] Task started: Blastn
[2024-01-25 20:05:15,007] [INFO] Running command: blastn -query GCF_003014695.1_ASM301469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference/reference_markers.fasta -out GCF_003014695.1_ASM301469v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:15,556] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:15,559] [INFO] Selected 11 target genomes.
[2024-01-25 20:05:15,559] [INFO] Target genome list was writen to GCF_003014695.1_ASM301469v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:15,576] [INFO] Task started: fastANI
[2024-01-25 20:05:15,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg49a2215e-fa68-4b45-b9a8-de87e57b8748/GCF_003014695.1_ASM301469v1_genomic.fna.gz --refList GCF_003014695.1_ASM301469v1_genomic.fna/target_genomes.txt --output GCF_003014695.1_ASM301469v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:32,129] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:32,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:32,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:32,136] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:05:32,136] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:32,136] [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
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	100.0	2728	2731	95	conclusive
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	84.9143	1939	2731	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	84.3443	1890	2731	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	83.5202	1572	2731	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	83.3933	1687	2731	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	83.3717	1686	2731	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	77.7394	469	2731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:32,137] [INFO] DFAST Taxonomy check result was written to GCF_003014695.1_ASM301469v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:32,138] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:32,138] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:32,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference/checkm_data
[2024-01-25 20:05:32,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:32,213] [INFO] Task started: CheckM
[2024-01-25 20:05:32,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003014695.1_ASM301469v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003014695.1_ASM301469v1_genomic.fna/checkm_input GCF_003014695.1_ASM301469v1_genomic.fna/checkm_result
[2024-01-25 20:07:09,957] [INFO] Task succeeded: CheckM
[2024-01-25 20:07:09,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:07:09,977] [INFO] ===== Completeness check finished =====
[2024-01-25 20:07:09,977] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:07:09,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003014695.1_ASM301469v1_genomic.fna/markers.fasta)
[2024-01-25 20:07:09,978] [INFO] Task started: Blastn
[2024-01-25 20:07:09,978] [INFO] Running command: blastn -query GCF_003014695.1_ASM301469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7548718-4008-4dbc-9185-ef801a2af50f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003014695.1_ASM301469v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:10,764] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:10,767] [INFO] Selected 7 target genomes.
[2024-01-25 20:07:10,767] [INFO] Target genome list was writen to GCF_003014695.1_ASM301469v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:07:10,773] [INFO] Task started: fastANI
[2024-01-25 20:07:10,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg49a2215e-fa68-4b45-b9a8-de87e57b8748/GCF_003014695.1_ASM301469v1_genomic.fna.gz --refList GCF_003014695.1_ASM301469v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003014695.1_ASM301469v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:24,857] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:24,863] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:07:24,863] [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_003014695.1	s__Dyadobacter jiangsuensis	100.0	2728	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017744695.1	s__Dyadobacter sp017744695	86.8755	2100	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109045.1	s__Dyadobacter sp900109045	85.4661	2014	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	84.9247	1937	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641595.1	s__Dyadobacter endophyticus	84.3547	1888	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	84.16	1703	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_000023125.1	s__Dyadobacter fermentans	83.5219	1572	2731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:24,864] [INFO] GTDB search result was written to GCF_003014695.1_ASM301469v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:24,865] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:24,867] [INFO] DFAST_QC result json was written to GCF_003014695.1_ASM301469v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:24,868] [INFO] DFAST_QC completed!
[2024-01-25 20:07:24,868] [INFO] Total running time: 0h2m49s