[2024-01-25 20:01:05,823] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:05,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:05,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference
[2024-01-25 20:01:06,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:06,935] [INFO] Task started: Prodigal
[2024-01-25 20:01:06,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a8c69c5-1acd-4e3a-babf-d6c3eb5e1248/GCF_029323795.1_ASM2932379v1_genomic.fna.gz | prodigal -d GCF_029323795.1_ASM2932379v1_genomic.fna/cds.fna -a GCF_029323795.1_ASM2932379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:23,843] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:23,844] [INFO] Task started: HMMsearch
[2024-01-25 20:01:23,844] [INFO] Running command: hmmsearch --tblout GCF_029323795.1_ASM2932379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference/reference_markers.hmm GCF_029323795.1_ASM2932379v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:24,124] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:24,125] [INFO] Found 6/6 markers.
[2024-01-25 20:01:24,164] [INFO] Query marker FASTA was written to GCF_029323795.1_ASM2932379v1_genomic.fna/markers.fasta
[2024-01-25 20:01:24,164] [INFO] Task started: Blastn
[2024-01-25 20:01:24,164] [INFO] Running command: blastn -query GCF_029323795.1_ASM2932379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference/reference_markers.fasta -out GCF_029323795.1_ASM2932379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:24,788] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:24,790] [INFO] Selected 13 target genomes.
[2024-01-25 20:01:24,791] [INFO] Target genome list was writen to GCF_029323795.1_ASM2932379v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:24,809] [INFO] Task started: fastANI
[2024-01-25 20:01:24,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8c69c5-1acd-4e3a-babf-d6c3eb5e1248/GCF_029323795.1_ASM2932379v1_genomic.fna.gz --refList GCF_029323795.1_ASM2932379v1_genomic.fna/target_genomes.txt --output GCF_029323795.1_ASM2932379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:36,567] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:36,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:36,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:36,577] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:01:36,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:01:36,577] [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
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	90.6054	1317	1688	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	82.0111	1025	1688	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	81.6679	1032	1688	95	below_threshold
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	81.3656	986	1688	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	81.2567	970	1688	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	81.1012	958	1688	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	79.5437	684	1688	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	79.462	718	1688	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.0605	72	1688	95	below_threshold
Maribacter algarum	strain=RZ26	GCA_005885635.1	2578118	2578118	type	True	76.8585	209	1688	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.5442	54	1688	95	below_threshold
Aquimarina pacifica	strain=SW150	GCA_000520955.1	1296415	1296415	type	True	76.3705	59	1688	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.1903	54	1688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:36,578] [INFO] DFAST Taxonomy check result was written to GCF_029323795.1_ASM2932379v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:36,579] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:36,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:36,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference/checkm_data
[2024-01-25 20:01:36,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:36,629] [INFO] Task started: CheckM
[2024-01-25 20:01:36,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_029323795.1_ASM2932379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_029323795.1_ASM2932379v1_genomic.fna/checkm_input GCF_029323795.1_ASM2932379v1_genomic.fna/checkm_result
[2024-01-25 20:02:25,065] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:25,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:25,090] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:25,090] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:25,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_029323795.1_ASM2932379v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:25,091] [INFO] Task started: Blastn
[2024-01-25 20:02:25,091] [INFO] Running command: blastn -query GCF_029323795.1_ASM2932379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc612b06b-97b0-48ed-babf-5cced12ef26d/dqc_reference/reference_markers_gtdb.fasta -out GCF_029323795.1_ASM2932379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:26,023] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:26,026] [INFO] Selected 9 target genomes.
[2024-01-25 20:02:26,026] [INFO] Target genome list was writen to GCF_029323795.1_ASM2932379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:26,039] [INFO] Task started: fastANI
[2024-01-25 20:02:26,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a8c69c5-1acd-4e3a-babf-d6c3eb5e1248/GCF_029323795.1_ASM2932379v1_genomic.fna.gz --refList GCF_029323795.1_ASM2932379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_029323795.1_ASM2932379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:36,444] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:36,451] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:02:36,451] [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_015330165.1	s__Zobellia sp015330165	90.6177	1316	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	-
GCF_018860745.1	s__Zobellia uliginosa_B	83.2728	1032	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	82.0111	1025	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_009725985.1	s__Zobellia amurskyensis	81.6715	1032	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_015330125.1	s__Zobellia sp015330125	81.3705	985	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_009725995.1	s__Zobellia laminariae	81.253	970	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603515.1	s__Zobellia sp018603515	81.0974	959	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156625.1	s__Zobellia uliginosa	79.5494	684	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	79.459	719	1688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:36,453] [INFO] GTDB search result was written to GCF_029323795.1_ASM2932379v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:36,453] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:36,459] [INFO] DFAST_QC result json was written to GCF_029323795.1_ASM2932379v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:36,460] [INFO] DFAST_QC completed!
[2024-01-25 20:02:36,460] [INFO] Total running time: 0h1m31s