[2023-06-28 05:54:26,331] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:54:26,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:54:26,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference
[2023-06-28 05:54:27,711] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:54:27,712] [INFO] Task started: Prodigal
[2023-06-28 05:54:27,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg18d7640d-69c3-4351-ac1b-99624a478074/GCA_944384575.1_E30_bin303_genomic.fna.gz | prodigal -d GCA_944384575.1_E30_bin303_genomic.fna/cds.fna -a GCA_944384575.1_E30_bin303_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:54:32,519] [INFO] Task succeeded: Prodigal
[2023-06-28 05:54:32,519] [INFO] Task started: HMMsearch
[2023-06-28 05:54:32,519] [INFO] Running command: hmmsearch --tblout GCA_944384575.1_E30_bin303_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference/reference_markers.hmm GCA_944384575.1_E30_bin303_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:54:32,770] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:54:32,772] [INFO] Found 6/6 markers.
[2023-06-28 05:54:32,793] [INFO] Query marker FASTA was written to GCA_944384575.1_E30_bin303_genomic.fna/markers.fasta
[2023-06-28 05:54:32,793] [INFO] Task started: Blastn
[2023-06-28 05:54:32,793] [INFO] Running command: blastn -query GCA_944384575.1_E30_bin303_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference/reference_markers.fasta -out GCA_944384575.1_E30_bin303_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:54:33,482] [INFO] Task succeeded: Blastn
[2023-06-28 05:54:33,487] [INFO] Selected 17 target genomes.
[2023-06-28 05:54:33,488] [INFO] Target genome list was writen to GCA_944384575.1_E30_bin303_genomic.fna/target_genomes.txt
[2023-06-28 05:54:33,491] [INFO] Task started: fastANI
[2023-06-28 05:54:33,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg18d7640d-69c3-4351-ac1b-99624a478074/GCA_944384575.1_E30_bin303_genomic.fna.gz --refList GCA_944384575.1_E30_bin303_genomic.fna/target_genomes.txt --output GCA_944384575.1_E30_bin303_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:54:46,069] [INFO] Task succeeded: fastANI
[2023-06-28 05:54:46,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:54:46,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:54:46,073] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:54:46,074] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:54:46,074] [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 05:54:46,076] [INFO] DFAST Taxonomy check result was written to GCA_944384575.1_E30_bin303_genomic.fna/tc_result.tsv
[2023-06-28 05:54:46,077] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:54:46,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:54:46,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference/checkm_data
[2023-06-28 05:54:46,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:54:46,106] [INFO] Task started: CheckM
[2023-06-28 05:54:46,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944384575.1_E30_bin303_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944384575.1_E30_bin303_genomic.fna/checkm_input GCA_944384575.1_E30_bin303_genomic.fna/checkm_result
[2023-06-28 05:55:07,656] [INFO] Task succeeded: CheckM
[2023-06-28 05:55:07,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:55:07,680] [INFO] ===== Completeness check finished =====
[2023-06-28 05:55:07,680] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:55:07,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944384575.1_E30_bin303_genomic.fna/markers.fasta)
[2023-06-28 05:55:07,681] [INFO] Task started: Blastn
[2023-06-28 05:55:07,681] [INFO] Running command: blastn -query GCA_944384575.1_E30_bin303_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e8231c4-9e77-4a88-970e-2093a6458785/dqc_reference/reference_markers_gtdb.fasta -out GCA_944384575.1_E30_bin303_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:55:08,741] [INFO] Task succeeded: Blastn
[2023-06-28 05:55:08,745] [INFO] Selected 16 target genomes.
[2023-06-28 05:55:08,745] [INFO] Target genome list was writen to GCA_944384575.1_E30_bin303_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:55:08,790] [INFO] Task started: fastANI
[2023-06-28 05:55:08,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg18d7640d-69c3-4351-ac1b-99624a478074/GCA_944384575.1_E30_bin303_genomic.fna.gz --refList GCA_944384575.1_E30_bin303_genomic.fna/target_genomes_gtdb.txt --output GCA_944384575.1_E30_bin303_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:55:14,851] [INFO] Task succeeded: fastANI
[2023-06-28 05:55:14,860] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:55:14,860] [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_003150035.1	s__QALR01 sp003150035	98.9488	449	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900553085.1	s__QALR01 sp900553085	78.9978	249	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	99.77	99.67	0.93	0.89	4	-
GCA_900552255.1	s__QALR01 sp900552255	78.8801	194	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	99.46	99.33	0.84	0.82	3	-
GCA_900542425.1	s__QALR01 sp900542425	78.5884	254	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937845.1	s__QALR01 sp017937845	76.441	60	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	98.42	98.41	0.91	0.89	3	-
GCA_017412045.1	s__QALR01 sp017412045	76.0766	57	579	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__QALR01	95.0	97.84	97.84	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-06-28 05:55:14,863] [INFO] GTDB search result was written to GCA_944384575.1_E30_bin303_genomic.fna/result_gtdb.tsv
[2023-06-28 05:55:14,863] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:55:14,875] [INFO] DFAST_QC result json was written to GCA_944384575.1_E30_bin303_genomic.fna/dqc_result.json
[2023-06-28 05:55:14,875] [INFO] DFAST_QC completed!
[2023-06-28 05:55:14,875] [INFO] Total running time: 0h0m49s