[2023-06-17 02:43:38,983] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:43:38,987] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:43:38,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference
[2023-06-17 02:43:40,611] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:43:40,619] [INFO] Task started: Prodigal
[2023-06-17 02:43:40,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b5a1bb-cb2a-47bb-87d8-e14213d6d793/GCA_003488405.1_ASM348840v1_genomic.fna.gz | prodigal -d GCA_003488405.1_ASM348840v1_genomic.fna/cds.fna -a GCA_003488405.1_ASM348840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:43:47,522] [INFO] Task succeeded: Prodigal
[2023-06-17 02:43:47,523] [INFO] Task started: HMMsearch
[2023-06-17 02:43:47,523] [INFO] Running command: hmmsearch --tblout GCA_003488405.1_ASM348840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference/reference_markers.hmm GCA_003488405.1_ASM348840v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:43:47,742] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:43:47,743] [INFO] Found 6/6 markers.
[2023-06-17 02:43:47,763] [INFO] Query marker FASTA was written to GCA_003488405.1_ASM348840v1_genomic.fna/markers.fasta
[2023-06-17 02:43:47,763] [INFO] Task started: Blastn
[2023-06-17 02:43:47,763] [INFO] Running command: blastn -query GCA_003488405.1_ASM348840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference/reference_markers.fasta -out GCA_003488405.1_ASM348840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:43:48,371] [INFO] Task succeeded: Blastn
[2023-06-17 02:43:48,376] [INFO] Selected 10 target genomes.
[2023-06-17 02:43:48,376] [INFO] Target genome list was writen to GCA_003488405.1_ASM348840v1_genomic.fna/target_genomes.txt
[2023-06-17 02:43:48,381] [INFO] Task started: fastANI
[2023-06-17 02:43:48,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b5a1bb-cb2a-47bb-87d8-e14213d6d793/GCA_003488405.1_ASM348840v1_genomic.fna.gz --refList GCA_003488405.1_ASM348840v1_genomic.fna/target_genomes.txt --output GCA_003488405.1_ASM348840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:43:55,667] [INFO] Task succeeded: fastANI
[2023-06-17 02:43:55,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:43:55,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:43:55,670] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:43:55,671] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:43:55,671] [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
--------------------------------------------------------------------------------
[2023-06-17 02:43:55,673] [INFO] DFAST Taxonomy check result was written to GCA_003488405.1_ASM348840v1_genomic.fna/tc_result.tsv
[2023-06-17 02:43:55,674] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:43:55,674] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:43:55,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference/checkm_data
[2023-06-17 02:43:55,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:43:55,691] [INFO] Task started: CheckM
[2023-06-17 02:43:55,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003488405.1_ASM348840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003488405.1_ASM348840v1_genomic.fna/checkm_input GCA_003488405.1_ASM348840v1_genomic.fna/checkm_result
[2023-06-17 02:44:22,382] [INFO] Task succeeded: CheckM
[2023-06-17 02:44:22,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:44:22,408] [INFO] ===== Completeness check finished =====
[2023-06-17 02:44:22,408] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:44:22,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003488405.1_ASM348840v1_genomic.fna/markers.fasta)
[2023-06-17 02:44:22,409] [INFO] Task started: Blastn
[2023-06-17 02:44:22,409] [INFO] Running command: blastn -query GCA_003488405.1_ASM348840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg947a22a6-b4ba-4e47-abc9-463301a55c0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_003488405.1_ASM348840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:23,224] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:23,229] [INFO] Selected 9 target genomes.
[2023-06-17 02:44:23,229] [INFO] Target genome list was writen to GCA_003488405.1_ASM348840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:44:23,235] [INFO] Task started: fastANI
[2023-06-17 02:44:23,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b5a1bb-cb2a-47bb-87d8-e14213d6d793/GCA_003488405.1_ASM348840v1_genomic.fna.gz --refList GCA_003488405.1_ASM348840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003488405.1_ASM348840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:44:25,290] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:25,300] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:44:25,300] [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_003518365.1	s__UBA12086 sp003518365	99.9158	357	370	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__UBA12086	95.0	99.86	99.74	0.95	0.92	7	conclusive
GCA_002784795.1	s__UBA12086 sp002784795	81.7706	156	370	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__UBA12086	95.0	99.70	99.59	0.85	0.84	3	-
GCA_001871445.1	s__UBA12086 sp001871445	81.2679	196	370	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__UBA12086	95.0	99.92	99.90	0.95	0.95	4	-
GCA_002792995.1	s__UBA12086 sp002792995	80.2654	153	370	d__Bacteria;p__Patescibacteria;c__ABY1;o__Magasanikbacterales;f__UBA922;g__UBA12086	95.0	99.78	99.78	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-17 02:44:25,303] [INFO] GTDB search result was written to GCA_003488405.1_ASM348840v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:44:25,303] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:44:25,306] [INFO] DFAST_QC result json was written to GCA_003488405.1_ASM348840v1_genomic.fna/dqc_result.json
[2023-06-17 02:44:25,306] [INFO] DFAST_QC completed!
[2023-06-17 02:44:25,306] [INFO] Total running time: 0h0m46s