[2023-06-27 07:57:45,451] [INFO] DFAST_QC pipeline started.
[2023-06-27 07:57:45,454] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 07:57:45,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference
[2023-06-27 07:57:46,704] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 07:57:46,705] [INFO] Task started: Prodigal
[2023-06-27 07:57:46,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg9e93e9d6-416a-4174-8931-58b079f71228/GCA_026005135.1_ASM2600513v1_genomic.fna.gz | prodigal -d GCA_026005135.1_ASM2600513v1_genomic.fna/cds.fna -a GCA_026005135.1_ASM2600513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 07:57:51,607] [INFO] Task succeeded: Prodigal
[2023-06-27 07:57:51,607] [INFO] Task started: HMMsearch
[2023-06-27 07:57:51,608] [INFO] Running command: hmmsearch --tblout GCA_026005135.1_ASM2600513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference/reference_markers.hmm GCA_026005135.1_ASM2600513v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 07:57:51,890] [INFO] Task succeeded: HMMsearch
[2023-06-27 07:57:51,891] [INFO] Found 6/6 markers.
[2023-06-27 07:57:51,929] [INFO] Query marker FASTA was written to GCA_026005135.1_ASM2600513v1_genomic.fna/markers.fasta
[2023-06-27 07:57:51,930] [INFO] Task started: Blastn
[2023-06-27 07:57:51,930] [INFO] Running command: blastn -query GCA_026005135.1_ASM2600513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference/reference_markers.fasta -out GCA_026005135.1_ASM2600513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:57:52,548] [INFO] Task succeeded: Blastn
[2023-06-27 07:57:52,552] [INFO] Selected 17 target genomes.
[2023-06-27 07:57:52,553] [INFO] Target genome list was writen to GCA_026005135.1_ASM2600513v1_genomic.fna/target_genomes.txt
[2023-06-27 07:57:52,562] [INFO] Task started: fastANI
[2023-06-27 07:57:52,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e93e9d6-416a-4174-8931-58b079f71228/GCA_026005135.1_ASM2600513v1_genomic.fna.gz --refList GCA_026005135.1_ASM2600513v1_genomic.fna/target_genomes.txt --output GCA_026005135.1_ASM2600513v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 07:58:01,862] [INFO] Task succeeded: fastANI
[2023-06-27 07:58:01,863] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 07:58:01,863] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 07:58:01,875] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 07:58:01,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 07:58:01,875] [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
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.0379	81	1132	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	74.9748	85	1132	95	below_threshold
Tenacibaculum jejuense	strain=type strain: KCTC 22618	GCA_900198195.1	584609	584609	type	True	74.9711	62	1132	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	74.9443	93	1132	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	74.9263	92	1132	95	below_threshold
Fusobacterium canifelinum	strain=FDAARGOS_1126	GCA_016724785.1	285729	285729	type	True	74.9216	74	1132	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	74.8483	73	1132	95	below_threshold
Mycoplasma capricolum subsp. capripneumoniae	strain=type strain: F38 = NCTC 10192	GCA_000953375.1	40480	2095	type	True	74.8362	60	1132	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001680885.1	1774273	1774273	type	True	74.7253	71	1132	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	74.7172	71	1132	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 07:58:01,877] [INFO] DFAST Taxonomy check result was written to GCA_026005135.1_ASM2600513v1_genomic.fna/tc_result.tsv
[2023-06-27 07:58:01,878] [INFO] ===== Taxonomy check completed =====
[2023-06-27 07:58:01,878] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 07:58:01,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference/checkm_data
[2023-06-27 07:58:01,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 07:58:01,914] [INFO] Task started: CheckM
[2023-06-27 07:58:01,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026005135.1_ASM2600513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026005135.1_ASM2600513v1_genomic.fna/checkm_input GCA_026005135.1_ASM2600513v1_genomic.fna/checkm_result
[2023-06-27 07:58:24,343] [INFO] Task succeeded: CheckM
[2023-06-27 07:58:24,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 07:58:24,373] [INFO] ===== Completeness check finished =====
[2023-06-27 07:58:24,373] [INFO] ===== Start GTDB Search =====
[2023-06-27 07:58:24,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026005135.1_ASM2600513v1_genomic.fna/markers.fasta)
[2023-06-27 07:58:24,374] [INFO] Task started: Blastn
[2023-06-27 07:58:24,374] [INFO] Running command: blastn -query GCA_026005135.1_ASM2600513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fad5364-4358-4fdc-a8e1-482e38a1a0cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_026005135.1_ASM2600513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 07:58:25,318] [INFO] Task succeeded: Blastn
[2023-06-27 07:58:25,324] [INFO] Selected 29 target genomes.
[2023-06-27 07:58:25,324] [INFO] Target genome list was writen to GCA_026005135.1_ASM2600513v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 07:58:25,350] [INFO] Task started: fastANI
[2023-06-27 07:58:25,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e93e9d6-416a-4174-8931-58b079f71228/GCA_026005135.1_ASM2600513v1_genomic.fna.gz --refList GCA_026005135.1_ASM2600513v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026005135.1_ASM2600513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 07:58:34,618] [INFO] Task succeeded: fastANI
[2023-06-27 07:58:34,632] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 07:58:34,633] [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_012569925.1	s__GCA-012562765 sp012569925	75.149	73	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__GCA-012562765	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128735.1	s__Buchnera aphidicola_L	75.1177	54	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__Buchnera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012570145.1	s__GCA-012562765 sp012570145	75.1118	71	1132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales_A;f__Enterobacteriaceae_A;g__GCA-012562765	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000182945.1	s__Fusobacterium vincentii	75.0086	72	1132	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	97.44	96.10	0.85	0.73	18	-
GCA_001880285.1	s__UJ101 sp001880285	74.9909	54	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UJ101;g__UJ101	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403635.1	s__Clostridium_P massiliamazoniense	74.9598	90	1132	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000007325.1	s__Fusobacterium nucleatum	74.9401	81	1132	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.30	95.23	0.93	0.85	13	-
GCF_016724785.1	s__Fusobacterium canifelinum	74.9141	69	1132	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Fusobacterium	95.0	98.22	98.13	0.90	0.87	3	-
GCA_017435465.1	s__SIG205 sp017435465	74.6729	64	1132	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419495.1	s__CAG-269 sp904419495	74.6522	62	1132	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 07:58:34,639] [INFO] GTDB search result was written to GCA_026005135.1_ASM2600513v1_genomic.fna/result_gtdb.tsv
[2023-06-27 07:58:34,640] [INFO] ===== GTDB Search completed =====
[2023-06-27 07:58:34,645] [INFO] DFAST_QC result json was written to GCA_026005135.1_ASM2600513v1_genomic.fna/dqc_result.json
[2023-06-27 07:58:34,645] [INFO] DFAST_QC completed!
[2023-06-27 07:58:34,645] [INFO] Total running time: 0h0m49s