[2023-06-28 01:42:56,414] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:42:56,420] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:42:56,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference
[2023-06-28 01:42:57,811] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:42:57,812] [INFO] Task started: Prodigal
[2023-06-28 01:42:57,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg493d5d12-308e-4d2e-a386-03128b9917de/GCA_026708035.1_ASM2670803v1_genomic.fna.gz | prodigal -d GCA_026708035.1_ASM2670803v1_genomic.fna/cds.fna -a GCA_026708035.1_ASM2670803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:43:08,647] [INFO] Task succeeded: Prodigal
[2023-06-28 01:43:08,647] [INFO] Task started: HMMsearch
[2023-06-28 01:43:08,647] [INFO] Running command: hmmsearch --tblout GCA_026708035.1_ASM2670803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference/reference_markers.hmm GCA_026708035.1_ASM2670803v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:43:08,902] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:43:08,904] [INFO] Found 6/6 markers.
[2023-06-28 01:43:08,933] [INFO] Query marker FASTA was written to GCA_026708035.1_ASM2670803v1_genomic.fna/markers.fasta
[2023-06-28 01:43:08,934] [INFO] Task started: Blastn
[2023-06-28 01:43:08,934] [INFO] Running command: blastn -query GCA_026708035.1_ASM2670803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference/reference_markers.fasta -out GCA_026708035.1_ASM2670803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:43:09,607] [INFO] Task succeeded: Blastn
[2023-06-28 01:43:09,611] [INFO] Selected 25 target genomes.
[2023-06-28 01:43:09,611] [INFO] Target genome list was writen to GCA_026708035.1_ASM2670803v1_genomic.fna/target_genomes.txt
[2023-06-28 01:43:09,627] [INFO] Task started: fastANI
[2023-06-28 01:43:09,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg493d5d12-308e-4d2e-a386-03128b9917de/GCA_026708035.1_ASM2670803v1_genomic.fna.gz --refList GCA_026708035.1_ASM2670803v1_genomic.fna/target_genomes.txt --output GCA_026708035.1_ASM2670803v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:43:31,755] [INFO] Task succeeded: fastANI
[2023-06-28 01:43:31,756] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:43:31,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:43:31,767] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:43:31,767] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 01:43:31,768] [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
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.7648	66	1133	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	74.7568	70	1133	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	74.7087	52	1133	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.7086	129	1133	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	74.6504	126	1133	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	74.6185	121	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 01:43:31,770] [INFO] DFAST Taxonomy check result was written to GCA_026708035.1_ASM2670803v1_genomic.fna/tc_result.tsv
[2023-06-28 01:43:31,770] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:43:31,771] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:43:31,771] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference/checkm_data
[2023-06-28 01:43:31,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:43:31,808] [INFO] Task started: CheckM
[2023-06-28 01:43:31,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708035.1_ASM2670803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708035.1_ASM2670803v1_genomic.fna/checkm_input GCA_026708035.1_ASM2670803v1_genomic.fna/checkm_result
[2023-06-28 01:44:05,298] [INFO] Task succeeded: CheckM
[2023-06-28 01:44:05,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:44:05,324] [INFO] ===== Completeness check finished =====
[2023-06-28 01:44:05,324] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:44:05,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708035.1_ASM2670803v1_genomic.fna/markers.fasta)
[2023-06-28 01:44:05,325] [INFO] Task started: Blastn
[2023-06-28 01:44:05,325] [INFO] Running command: blastn -query GCA_026708035.1_ASM2670803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff02be51-7d4f-4852-b80c-1bd3131a50f4/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708035.1_ASM2670803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:44:06,213] [INFO] Task succeeded: Blastn
[2023-06-28 01:44:06,234] [INFO] Selected 23 target genomes.
[2023-06-28 01:44:06,234] [INFO] Target genome list was writen to GCA_026708035.1_ASM2670803v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:44:06,251] [INFO] Task started: fastANI
[2023-06-28 01:44:06,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg493d5d12-308e-4d2e-a386-03128b9917de/GCA_026708035.1_ASM2670803v1_genomic.fna.gz --refList GCA_026708035.1_ASM2670803v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708035.1_ASM2670803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:44:20,577] [INFO] Task succeeded: fastANI
[2023-06-28 01:44:20,587] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 01:44:20,587] [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_011523785.1	s__UBA11872 sp011523785	78.0226	213	1133	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009839425.1	s__UBA11872 sp009839425	76.9715	194	1133	d__Bacteria;p__Chloroflexota;c__UBA11872;o__UBA11872;f__UBA11872;g__UBA11872	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367385.1	s__SpSt-583 sp011367385	74.8939	77	1133	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003762835.1	s__Plantactinospora sp003762835	74.7763	79	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091555.1	s__Micromonospora mirobrigensis	74.5889	103	1133	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:44:20,589] [INFO] GTDB search result was written to GCA_026708035.1_ASM2670803v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:44:20,589] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:44:20,592] [INFO] DFAST_QC result json was written to GCA_026708035.1_ASM2670803v1_genomic.fna/dqc_result.json
[2023-06-28 01:44:20,592] [INFO] DFAST_QC completed!
[2023-06-28 01:44:20,592] [INFO] Total running time: 0h1m24s