[2023-06-29 19:13:45,357] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:45,360] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:45,360] [INFO] DQC Reference Directory: /var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference
[2023-06-29 19:13:46,923] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:46,924] [INFO] Task started: Prodigal
[2023-06-29 19:13:46,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg4701e15f-9ffe-40d4-b6dd-ea78c62ca160/GCA_021638385.1_ASM2163838v1_genomic.fna.gz | prodigal -d GCA_021638385.1_ASM2163838v1_genomic.fna/cds.fna -a GCA_021638385.1_ASM2163838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:51,750] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:51,751] [INFO] Task started: HMMsearch
[2023-06-29 19:13:51,751] [INFO] Running command: hmmsearch --tblout GCA_021638385.1_ASM2163838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference/reference_markers.hmm GCA_021638385.1_ASM2163838v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:51,978] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:51,979] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4701e15f-9ffe-40d4-b6dd-ea78c62ca160/GCA_021638385.1_ASM2163838v1_genomic.fna.gz]
[2023-06-29 19:13:52,004] [INFO] Query marker FASTA was written to GCA_021638385.1_ASM2163838v1_genomic.fna/markers.fasta
[2023-06-29 19:13:52,005] [INFO] Task started: Blastn
[2023-06-29 19:13:52,005] [INFO] Running command: blastn -query GCA_021638385.1_ASM2163838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference/reference_markers.fasta -out GCA_021638385.1_ASM2163838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:52,706] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:52,721] [INFO] Selected 19 target genomes.
[2023-06-29 19:13:52,721] [INFO] Target genome list was writen to GCA_021638385.1_ASM2163838v1_genomic.fna/target_genomes.txt
[2023-06-29 19:13:52,722] [INFO] Task started: fastANI
[2023-06-29 19:13:52,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg4701e15f-9ffe-40d4-b6dd-ea78c62ca160/GCA_021638385.1_ASM2163838v1_genomic.fna.gz --refList GCA_021638385.1_ASM2163838v1_genomic.fna/target_genomes.txt --output GCA_021638385.1_ASM2163838v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:06,289] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:06,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:06,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:06,298] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:14:06,298] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 19:14:06,298] [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
--------------------------------------------------------------------------------
[2023-06-29 19:14:06,301] [INFO] DFAST Taxonomy check result was written to GCA_021638385.1_ASM2163838v1_genomic.fna/tc_result.tsv
[2023-06-29 19:14:06,302] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:06,302] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:06,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference/checkm_data
[2023-06-29 19:14:06,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:06,331] [INFO] Task started: CheckM
[2023-06-29 19:14:06,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021638385.1_ASM2163838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021638385.1_ASM2163838v1_genomic.fna/checkm_input GCA_021638385.1_ASM2163838v1_genomic.fna/checkm_result
[2023-06-29 19:14:27,504] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:27,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:27,525] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:27,526] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:27,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021638385.1_ASM2163838v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:27,527] [INFO] Task started: Blastn
[2023-06-29 19:14:27,527] [INFO] Running command: blastn -query GCA_021638385.1_ASM2163838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge470e9d4-9709-492b-b2e6-69617e51aece/dqc_reference/reference_markers_gtdb.fasta -out GCA_021638385.1_ASM2163838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:28,364] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:28,368] [INFO] Selected 20 target genomes.
[2023-06-29 19:14:28,369] [INFO] Target genome list was writen to GCA_021638385.1_ASM2163838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:28,375] [INFO] Task started: fastANI
[2023-06-29 19:14:28,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg4701e15f-9ffe-40d4-b6dd-ea78c62ca160/GCA_021638385.1_ASM2163838v1_genomic.fna.gz --refList GCA_021638385.1_ASM2163838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021638385.1_ASM2163838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:35,354] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:35,365] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:14:35,366] [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_003150135.1	s__CAG-448 sp003150135	98.2158	347	382	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	98.32	98.19	0.84	0.75	5	conclusive
GCA_900768535.1	s__UMGS1865 sp900768535	78.0582	60	382	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS1865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938885.1	s__CAG-448 sp017938885	77.7278	63	382	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063685.1	s__CAG-448 sp015063685	77.621	53	382	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017483125.1	s__CAG-448 sp017483125	77.3743	67	382	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-448	95.0	96.34	96.34	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:35,368] [INFO] GTDB search result was written to GCA_021638385.1_ASM2163838v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:35,369] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:35,372] [INFO] DFAST_QC result json was written to GCA_021638385.1_ASM2163838v1_genomic.fna/dqc_result.json
[2023-06-29 19:14:35,372] [INFO] DFAST_QC completed!
[2023-06-29 19:14:35,372] [INFO] Total running time: 0h0m50s