[2023-06-26 23:15:17,729] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:15:17,731] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:15:17,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference
[2023-06-26 23:15:19,632] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:15:19,633] [INFO] Task started: Prodigal
[2023-06-26 23:15:19,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c5b1bbf-aa01-4899-90a0-2aac7c086592/GCA_026004015.1_ASM2600401v1_genomic.fna.gz | prodigal -d GCA_026004015.1_ASM2600401v1_genomic.fna/cds.fna -a GCA_026004015.1_ASM2600401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:15:22,218] [INFO] Task succeeded: Prodigal
[2023-06-26 23:15:22,219] [INFO] Task started: HMMsearch
[2023-06-26 23:15:22,219] [INFO] Running command: hmmsearch --tblout GCA_026004015.1_ASM2600401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference/reference_markers.hmm GCA_026004015.1_ASM2600401v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:15:22,422] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:15:22,423] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8c5b1bbf-aa01-4899-90a0-2aac7c086592/GCA_026004015.1_ASM2600401v1_genomic.fna.gz]
[2023-06-26 23:15:22,437] [INFO] Query marker FASTA was written to GCA_026004015.1_ASM2600401v1_genomic.fna/markers.fasta
[2023-06-26 23:15:22,437] [INFO] Task started: Blastn
[2023-06-26 23:15:22,437] [INFO] Running command: blastn -query GCA_026004015.1_ASM2600401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference/reference_markers.fasta -out GCA_026004015.1_ASM2600401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:15:23,695] [INFO] Task succeeded: Blastn
[2023-06-26 23:15:23,700] [INFO] Selected 15 target genomes.
[2023-06-26 23:15:23,700] [INFO] Target genome list was writen to GCA_026004015.1_ASM2600401v1_genomic.fna/target_genomes.txt
[2023-06-26 23:15:23,703] [INFO] Task started: fastANI
[2023-06-26 23:15:23,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c5b1bbf-aa01-4899-90a0-2aac7c086592/GCA_026004015.1_ASM2600401v1_genomic.fna.gz --refList GCA_026004015.1_ASM2600401v1_genomic.fna/target_genomes.txt --output GCA_026004015.1_ASM2600401v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:15:33,599] [INFO] Task succeeded: fastANI
[2023-06-26 23:15:33,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:15:33,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:15:33,608] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:15:33,608] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 23:15:33,609] [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
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.9846	124	453	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	74.8897	71	453	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	74.8841	53	453	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	74.8763	54	453	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.873	96	453	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	74.8576	75	453	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	74.8215	85	453	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.7468	98	453	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	74.742	78	453	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	74.7381	79	453	95	below_threshold
Halorubrum distributum	strain=JCM 9100	GCA_000337055.1	29283	29283	suspected-type	True	74.6845	65	453	95	below_threshold
Halorubrum distributum	strain=JCM 10118	GCA_000337335.1	29283	29283	suspected-type	True	74.6487	65	453	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 23:15:33,610] [INFO] DFAST Taxonomy check result was written to GCA_026004015.1_ASM2600401v1_genomic.fna/tc_result.tsv
[2023-06-26 23:15:33,611] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:15:33,611] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:15:33,611] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference/checkm_data
[2023-06-26 23:15:33,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:15:33,627] [INFO] Task started: CheckM
[2023-06-26 23:15:33,627] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026004015.1_ASM2600401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026004015.1_ASM2600401v1_genomic.fna/checkm_input GCA_026004015.1_ASM2600401v1_genomic.fna/checkm_result
[2023-06-26 23:15:49,169] [INFO] Task succeeded: CheckM
[2023-06-26 23:15:49,171] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:15:49,187] [INFO] ===== Completeness check finished =====
[2023-06-26 23:15:49,187] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:15:49,188] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026004015.1_ASM2600401v1_genomic.fna/markers.fasta)
[2023-06-26 23:15:49,188] [INFO] Task started: Blastn
[2023-06-26 23:15:49,188] [INFO] Running command: blastn -query GCA_026004015.1_ASM2600401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg870d548c-997b-4e39-b51a-203a85dca4e0/dqc_reference/reference_markers_gtdb.fasta -out GCA_026004015.1_ASM2600401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:15:49,729] [INFO] Task succeeded: Blastn
[2023-06-26 23:15:49,732] [INFO] Selected 14 target genomes.
[2023-06-26 23:15:49,732] [INFO] Target genome list was writen to GCA_026004015.1_ASM2600401v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:15:49,735] [INFO] Task started: fastANI
[2023-06-26 23:15:49,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c5b1bbf-aa01-4899-90a0-2aac7c086592/GCA_026004015.1_ASM2600401v1_genomic.fna.gz --refList GCA_026004015.1_ASM2600401v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026004015.1_ASM2600401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:15:56,404] [INFO] Task succeeded: fastANI
[2023-06-26 23:15:56,414] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:15:56,414] [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_001795245.1	s__UBA5189 sp001795245	78.4007	190	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297395.1	s__UBA5189 sp004297395	78.3908	183	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200675.1	s__UBA5189 sp016200675	78.3111	141	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200665.1	s__UBA5189 sp016200665	78.1428	149	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478725.1	s__C-114 sp015478725	77.7916	182	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026785.1	s__UBA5189 sp012026785	77.6989	173	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881055.1	s__C-114 sp005881055	77.6363	131	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__C-114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882635.1	s__CF-46 sp005882635	77.6055	182	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250155.1	s__UBA5189 sp003250155	77.5405	114	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	99.47	99.47	0.88	0.88	2	-
GCA_005889475.1	s__UBA5189 sp005889475	77.2874	134	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141955.1	s__Fen-1039 sp003141955	77.2307	85	453	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_903928275.1	s__CAIYQJ01 sp903928275	76.9923	122	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIYQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157175.1	s__Fen-1039 sp003157175	76.4436	60	453	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Fen-1039	95.0	98.79	98.79	0.73	0.73	2	-
GCA_003171035.1	s__Fen-1039 sp003171035	76.2476	64	453	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	-
--------------------------------------------------------------------------------
[2023-06-26 23:15:56,416] [INFO] GTDB search result was written to GCA_026004015.1_ASM2600401v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:15:56,417] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:15:56,420] [INFO] DFAST_QC result json was written to GCA_026004015.1_ASM2600401v1_genomic.fna/dqc_result.json
[2023-06-26 23:15:56,420] [INFO] DFAST_QC completed!
[2023-06-26 23:15:56,420] [INFO] Total running time: 0h0m39s