[2023-06-17 07:12:08,141] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:12:08,144] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:12:08,144] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference
[2023-06-17 07:12:11,391] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:12:11,392] [INFO] Task started: Prodigal
[2023-06-17 07:12:11,392] [INFO] Running command: gunzip -c /var/lib/cwl/stge14367f0-5e97-44b5-aae8-729597853113/GCA_003170855.1_20110800_E2D_genomic.fna.gz | prodigal -d GCA_003170855.1_20110800_E2D_genomic.fna/cds.fna -a GCA_003170855.1_20110800_E2D_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:12:20,332] [INFO] Task succeeded: Prodigal
[2023-06-17 07:12:20,333] [INFO] Task started: HMMsearch
[2023-06-17 07:12:20,333] [INFO] Running command: hmmsearch --tblout GCA_003170855.1_20110800_E2D_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference/reference_markers.hmm GCA_003170855.1_20110800_E2D_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:12:20,560] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:12:20,562] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge14367f0-5e97-44b5-aae8-729597853113/GCA_003170855.1_20110800_E2D_genomic.fna.gz]
[2023-06-17 07:12:20,598] [INFO] Query marker FASTA was written to GCA_003170855.1_20110800_E2D_genomic.fna/markers.fasta
[2023-06-17 07:12:20,599] [INFO] Task started: Blastn
[2023-06-17 07:12:20,599] [INFO] Running command: blastn -query GCA_003170855.1_20110800_E2D_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference/reference_markers.fasta -out GCA_003170855.1_20110800_E2D_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:12:21,220] [INFO] Task succeeded: Blastn
[2023-06-17 07:12:21,226] [INFO] Selected 20 target genomes.
[2023-06-17 07:12:21,226] [INFO] Target genome list was writen to GCA_003170855.1_20110800_E2D_genomic.fna/target_genomes.txt
[2023-06-17 07:12:21,235] [INFO] Task started: fastANI
[2023-06-17 07:12:21,235] [INFO] Running command: fastANI --query /var/lib/cwl/stge14367f0-5e97-44b5-aae8-729597853113/GCA_003170855.1_20110800_E2D_genomic.fna.gz --refList GCA_003170855.1_20110800_E2D_genomic.fna/target_genomes.txt --output GCA_003170855.1_20110800_E2D_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:12:36,853] [INFO] Task succeeded: fastANI
[2023-06-17 07:12:36,854] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:12:36,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:12:36,864] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:12:36,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 07:12:36,865] [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
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.9113	80	1066	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	74.8921	125	1066	95	below_threshold
Actinomadura litoris	strain=NEAU-AAG5	GCA_009733595.1	2678616	2678616	type	True	74.8064	115	1066	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	74.7565	111	1066	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	74.7365	100	1066	95	below_threshold
Mangrovactinospora gilvigriseus	strain=MUSC 26	GCA_001879105.1	1428644	1428644	type	True	74.72	62	1066	95	below_threshold
Actinomadura soli	strain=14C53	GCA_005889715.1	2508997	2508997	type	True	74.6654	90	1066	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:12:36,868] [INFO] DFAST Taxonomy check result was written to GCA_003170855.1_20110800_E2D_genomic.fna/tc_result.tsv
[2023-06-17 07:12:36,868] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:12:36,868] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:12:36,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference/checkm_data
[2023-06-17 07:12:36,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:12:36,913] [INFO] Task started: CheckM
[2023-06-17 07:12:36,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003170855.1_20110800_E2D_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003170855.1_20110800_E2D_genomic.fna/checkm_input GCA_003170855.1_20110800_E2D_genomic.fna/checkm_result
[2023-06-17 07:13:09,945] [INFO] Task succeeded: CheckM
[2023-06-17 07:13:09,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.34%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 07:13:09,989] [INFO] ===== Completeness check finished =====
[2023-06-17 07:13:09,989] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:13:09,990] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003170855.1_20110800_E2D_genomic.fna/markers.fasta)
[2023-06-17 07:13:09,990] [INFO] Task started: Blastn
[2023-06-17 07:13:09,990] [INFO] Running command: blastn -query GCA_003170855.1_20110800_E2D_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd717b9f-cd23-403a-94ce-9b8cc134df35/dqc_reference/reference_markers_gtdb.fasta -out GCA_003170855.1_20110800_E2D_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:13:10,858] [INFO] Task succeeded: Blastn
[2023-06-17 07:13:10,863] [INFO] Selected 13 target genomes.
[2023-06-17 07:13:10,864] [INFO] Target genome list was writen to GCA_003170855.1_20110800_E2D_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:13:10,873] [INFO] Task started: fastANI
[2023-06-17 07:13:10,874] [INFO] Running command: fastANI --query /var/lib/cwl/stge14367f0-5e97-44b5-aae8-729597853113/GCA_003170855.1_20110800_E2D_genomic.fna.gz --refList GCA_003170855.1_20110800_E2D_genomic.fna/target_genomes_gtdb.txt --output GCA_003170855.1_20110800_E2D_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:13:18,100] [INFO] Task succeeded: fastANI
[2023-06-17 07:13:18,112] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 07:13:18,112] [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_003158495.1	s__Fen-1039 sp003158495	81.3661	532	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142755.1	s__Fen-1039 sp003142755	81.012	454	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.72	99.72	0.87	0.87	2	-
GCA_003171255.1	s__Fen-1039 sp003171255	80.938	451	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165675.1	s__Fen-1039 sp003165675	80.6366	430	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.52	99.29	0.91	0.88	12	-
GCA_003141245.1	s__Fen-1039 sp003141245	80.5698	422	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141955.1	s__Fen-1039 sp003141955	80.5537	435	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.62	99.62	0.93	0.93	2	-
GCA_003141455.1	s__Fen-1039 sp003141455	80.2237	447	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.88	99.88	0.96	0.96	2	-
GCA_003171065.1	s__Fen-1039 sp003171065	80.1558	425	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.79	99.79	0.91	0.91	2	-
GCA_003156975.1	s__Fen-1039 sp003156975	80.1282	376	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003171035.1	s__Fen-1039 sp003171035	80.0498	394	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157875.1	s__Fen-1039 sp003157875	80.0264	447	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158295.1	s__Fen-1039 sp003158295	79.8508	377	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	99.78	99.69	0.93	0.93	5	-
GCA_017881885.1	s__Fen-1039 sp017881885	79.6358	354	1066	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 07:13:18,114] [INFO] GTDB search result was written to GCA_003170855.1_20110800_E2D_genomic.fna/result_gtdb.tsv
[2023-06-17 07:13:18,115] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:13:18,132] [INFO] DFAST_QC result json was written to GCA_003170855.1_20110800_E2D_genomic.fna/dqc_result.json
[2023-06-17 07:13:18,132] [INFO] DFAST_QC completed!
[2023-06-17 07:13:18,133] [INFO] Total running time: 0h1m10s