[2023-06-28 19:34:02,378] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:34:02,380] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:34:02,380] [INFO] DQC Reference Directory: /var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference
[2023-06-28 19:34:03,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:34:03,633] [INFO] Task started: Prodigal
[2023-06-28 19:34:03,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg40d038d3-29a1-4f30-8781-b9d0f5abd479/GCA_002708885.1_ASM270888v1_genomic.fna.gz | prodigal -d GCA_002708885.1_ASM270888v1_genomic.fna/cds.fna -a GCA_002708885.1_ASM270888v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:34:17,824] [INFO] Task succeeded: Prodigal
[2023-06-28 19:34:17,824] [INFO] Task started: HMMsearch
[2023-06-28 19:34:17,825] [INFO] Running command: hmmsearch --tblout GCA_002708885.1_ASM270888v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference/reference_markers.hmm GCA_002708885.1_ASM270888v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:34:18,082] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:34:18,083] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40d038d3-29a1-4f30-8781-b9d0f5abd479/GCA_002708885.1_ASM270888v1_genomic.fna.gz]
[2023-06-28 19:34:18,114] [INFO] Query marker FASTA was written to GCA_002708885.1_ASM270888v1_genomic.fna/markers.fasta
[2023-06-28 19:34:18,115] [INFO] Task started: Blastn
[2023-06-28 19:34:18,115] [INFO] Running command: blastn -query GCA_002708885.1_ASM270888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference/reference_markers.fasta -out GCA_002708885.1_ASM270888v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:34:18,671] [INFO] Task succeeded: Blastn
[2023-06-28 19:34:18,676] [INFO] Selected 14 target genomes.
[2023-06-28 19:34:18,676] [INFO] Target genome list was writen to GCA_002708885.1_ASM270888v1_genomic.fna/target_genomes.txt
[2023-06-28 19:34:18,683] [INFO] Task started: fastANI
[2023-06-28 19:34:18,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d038d3-29a1-4f30-8781-b9d0f5abd479/GCA_002708885.1_ASM270888v1_genomic.fna.gz --refList GCA_002708885.1_ASM270888v1_genomic.fna/target_genomes.txt --output GCA_002708885.1_ASM270888v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:34:26,048] [INFO] Task succeeded: fastANI
[2023-06-28 19:34:26,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:34:26,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:34:26,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:34:26,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 19:34:26,051] [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
--------------------------------------------------------------------------------
[2023-06-28 19:34:26,054] [INFO] DFAST Taxonomy check result was written to GCA_002708885.1_ASM270888v1_genomic.fna/tc_result.tsv
[2023-06-28 19:34:26,054] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:34:26,055] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:34:26,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference/checkm_data
[2023-06-28 19:34:26,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:34:26,097] [INFO] Task started: CheckM
[2023-06-28 19:34:26,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708885.1_ASM270888v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708885.1_ASM270888v1_genomic.fna/checkm_input GCA_002708885.1_ASM270888v1_genomic.fna/checkm_result
[2023-06-28 19:35:12,909] [INFO] Task succeeded: CheckM
[2023-06-28 19:35:12,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 7.41%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 19:35:12,935] [INFO] ===== Completeness check finished =====
[2023-06-28 19:35:12,935] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:35:12,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708885.1_ASM270888v1_genomic.fna/markers.fasta)
[2023-06-28 19:35:12,936] [INFO] Task started: Blastn
[2023-06-28 19:35:12,936] [INFO] Running command: blastn -query GCA_002708885.1_ASM270888v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg63a22f2a-ecb3-44f5-9372-daa1416488ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708885.1_ASM270888v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:35:13,629] [INFO] Task succeeded: Blastn
[2023-06-28 19:35:13,634] [INFO] Selected 12 target genomes.
[2023-06-28 19:35:13,635] [INFO] Target genome list was writen to GCA_002708885.1_ASM270888v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:35:13,646] [INFO] Task started: fastANI
[2023-06-28 19:35:13,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d038d3-29a1-4f30-8781-b9d0f5abd479/GCA_002708885.1_ASM270888v1_genomic.fna.gz --refList GCA_002708885.1_ASM270888v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708885.1_ASM270888v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:35:21,023] [INFO] Task succeeded: fastANI
[2023-06-28 19:35:21,033] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:35:21,033] [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
GCA_002708885.1	s__EC70 sp002708885	100.0	1071	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.95	98.84	0.89	0.88	3	conclusive
GCA_004211885.1	s__EC70 sp004211885	83.1647	731	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591645.1	s__EC70 sp902591645	82.9989	444	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	95.33	95.33	0.70	0.70	2	-
GCA_014239335.1	s__EC70 sp014239335	82.2394	530	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	98.68	98.68	0.76	0.76	2	-
GCA_012960505.1	s__EC70 sp012960505	81.9829	785	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	99.96	99.96	0.97	0.97	2	-
GCA_013213965.1	s__EC70 sp013213965	81.2397	548	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684575.1	s__EC70 sp002684575	76.5758	65	1081	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__EC70	95.0	96.27	95.80	0.72	0.71	3	-
--------------------------------------------------------------------------------
[2023-06-28 19:35:21,035] [INFO] GTDB search result was written to GCA_002708885.1_ASM270888v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:35:21,035] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:35:21,038] [INFO] DFAST_QC result json was written to GCA_002708885.1_ASM270888v1_genomic.fna/dqc_result.json
[2023-06-28 19:35:21,038] [INFO] DFAST_QC completed!
[2023-06-28 19:35:21,038] [INFO] Total running time: 0h1m19s