[2023-06-26 22:36:51,074] [INFO] DFAST_QC pipeline started.
[2023-06-26 22:36:51,084] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 22:36:51,085] [INFO] DQC Reference Directory: /var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference
[2023-06-26 22:36:52,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 22:36:52,475] [INFO] Task started: Prodigal
[2023-06-26 22:36:52,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b94c2de-39fc-41ff-b7ed-08c175437983/GCA_002385985.1_ASM238598v1_genomic.fna.gz | prodigal -d GCA_002385985.1_ASM238598v1_genomic.fna/cds.fna -a GCA_002385985.1_ASM238598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 22:37:00,038] [INFO] Task succeeded: Prodigal
[2023-06-26 22:37:00,039] [INFO] Task started: HMMsearch
[2023-06-26 22:37:00,039] [INFO] Running command: hmmsearch --tblout GCA_002385985.1_ASM238598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference/reference_markers.hmm GCA_002385985.1_ASM238598v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 22:37:00,361] [INFO] Task succeeded: HMMsearch
[2023-06-26 22:37:00,363] [INFO] Found 6/6 markers.
[2023-06-26 22:37:00,397] [INFO] Query marker FASTA was written to GCA_002385985.1_ASM238598v1_genomic.fna/markers.fasta
[2023-06-26 22:37:00,397] [INFO] Task started: Blastn
[2023-06-26 22:37:00,397] [INFO] Running command: blastn -query GCA_002385985.1_ASM238598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference/reference_markers.fasta -out GCA_002385985.1_ASM238598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:37:01,069] [INFO] Task succeeded: Blastn
[2023-06-26 22:37:01,073] [INFO] Selected 26 target genomes.
[2023-06-26 22:37:01,074] [INFO] Target genome list was writen to GCA_002385985.1_ASM238598v1_genomic.fna/target_genomes.txt
[2023-06-26 22:37:01,076] [INFO] Task started: fastANI
[2023-06-26 22:37:01,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b94c2de-39fc-41ff-b7ed-08c175437983/GCA_002385985.1_ASM238598v1_genomic.fna.gz --refList GCA_002385985.1_ASM238598v1_genomic.fna/target_genomes.txt --output GCA_002385985.1_ASM238598v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 22:37:22,005] [INFO] Task succeeded: fastANI
[2023-06-26 22:37:22,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 22:37:22,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 22:37:22,015] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 22:37:22,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 22:37:22,015] [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
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	76.576	113	872	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	76.5588	146	872	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	76.5315	144	872	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	76.0909	93	872	95	below_threshold
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	75.3287	65	872	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	74.904	98	872	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	74.8814	59	872	95	below_threshold
Actinomadura cremea	strain=JCM 3308	GCA_014648495.1	1991	1991	type	True	74.877	62	872	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.8727	51	872	95	below_threshold
Actinomadura chibensis	strain=NBRC 106107	GCA_001552135.1	392828	392828	type	True	74.7732	66	872	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 22:37:22,018] [INFO] DFAST Taxonomy check result was written to GCA_002385985.1_ASM238598v1_genomic.fna/tc_result.tsv
[2023-06-26 22:37:22,019] [INFO] ===== Taxonomy check completed =====
[2023-06-26 22:37:22,019] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 22:37:22,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference/checkm_data
[2023-06-26 22:37:22,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 22:37:22,060] [INFO] Task started: CheckM
[2023-06-26 22:37:22,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002385985.1_ASM238598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002385985.1_ASM238598v1_genomic.fna/checkm_input GCA_002385985.1_ASM238598v1_genomic.fna/checkm_result
[2023-06-26 22:37:49,590] [INFO] Task succeeded: CheckM
[2023-06-26 22:37:49,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 22:37:49,622] [INFO] ===== Completeness check finished =====
[2023-06-26 22:37:49,622] [INFO] ===== Start GTDB Search =====
[2023-06-26 22:37:49,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002385985.1_ASM238598v1_genomic.fna/markers.fasta)
[2023-06-26 22:37:49,623] [INFO] Task started: Blastn
[2023-06-26 22:37:49,623] [INFO] Running command: blastn -query GCA_002385985.1_ASM238598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2bd5d50-2892-44db-ae8b-692dd7307f59/dqc_reference/reference_markers_gtdb.fasta -out GCA_002385985.1_ASM238598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 22:37:50,566] [INFO] Task succeeded: Blastn
[2023-06-26 22:37:50,571] [INFO] Selected 29 target genomes.
[2023-06-26 22:37:50,572] [INFO] Target genome list was writen to GCA_002385985.1_ASM238598v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 22:37:50,589] [INFO] Task started: fastANI
[2023-06-26 22:37:50,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b94c2de-39fc-41ff-b7ed-08c175437983/GCA_002385985.1_ASM238598v1_genomic.fna.gz --refList GCA_002385985.1_ASM238598v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002385985.1_ASM238598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 22:38:10,990] [INFO] Task succeeded: fastANI
[2023-06-26 22:38:11,008] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-26 22:38:11,008] [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_002385985.1	s__UBA3924 sp002385985	99.9999	865	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	conclusive
GCA_002298885.1	s__UBA700 sp002298885	77.0277	113	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA700	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050235.1	s__Longilinea arvoryzae	76.5565	114	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Longilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191875.1	s__SCUK01 sp016191875	76.5285	93	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA11579;g__SCUK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213105.1	s__JACPVF01 sp016213105	76.4885	109	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JACPVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798515.1	s__JAAZNB01 sp012798515	76.4382	123	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__JAAZNB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428565.1	s__UBA6092 sp002428565	76.438	103	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	76.4231	86	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367385.1	s__SpSt-583 sp011367385	76.3546	129	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__SpSt-583	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011176535.1	s__DUEP01 sp011176535	76.3234	52	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRMV01;g__DUEP01	95.0	99.79	99.71	0.93	0.89	3	-
GCA_002418215.1	s__UBA5796 sp002418215	76.2256	107	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA5796	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934715.1	s__JAFGSI01 sp016934715	76.1918	93	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JAFGSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367365.1	s__DSYU01 sp011367365	76.1788	106	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__DSYU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306115.1	s__Ornatilinea apprima	76.1056	92	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Ornatilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935755.1	s__JAFGQI01 sp016935755	75.7893	56	872	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__JAFGQI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 22:38:11,011] [INFO] GTDB search result was written to GCA_002385985.1_ASM238598v1_genomic.fna/result_gtdb.tsv
[2023-06-26 22:38:11,012] [INFO] ===== GTDB Search completed =====
[2023-06-26 22:38:11,016] [INFO] DFAST_QC result json was written to GCA_002385985.1_ASM238598v1_genomic.fna/dqc_result.json
[2023-06-26 22:38:11,016] [INFO] DFAST_QC completed!
[2023-06-26 22:38:11,016] [INFO] Total running time: 0h1m20s