[2023-06-29 01:46:08,253] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:46:08,256] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:46:08,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference
[2023-06-29 01:46:09,782] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:46:09,784] [INFO] Task started: Prodigal
[2023-06-29 01:46:09,784] [INFO] Running command: gunzip -c /var/lib/cwl/stge9c10230-1e0c-4c73-8711-575b0d916851/GCA_027396385.1_ASM2739638v1_genomic.fna.gz | prodigal -d GCA_027396385.1_ASM2739638v1_genomic.fna/cds.fna -a GCA_027396385.1_ASM2739638v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:46:16,230] [INFO] Task succeeded: Prodigal
[2023-06-29 01:46:16,230] [INFO] Task started: HMMsearch
[2023-06-29 01:46:16,230] [INFO] Running command: hmmsearch --tblout GCA_027396385.1_ASM2739638v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference/reference_markers.hmm GCA_027396385.1_ASM2739638v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:46:16,466] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:46:16,468] [INFO] Found 6/6 markers.
[2023-06-29 01:46:16,495] [INFO] Query marker FASTA was written to GCA_027396385.1_ASM2739638v1_genomic.fna/markers.fasta
[2023-06-29 01:46:16,495] [INFO] Task started: Blastn
[2023-06-29 01:46:16,495] [INFO] Running command: blastn -query GCA_027396385.1_ASM2739638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference/reference_markers.fasta -out GCA_027396385.1_ASM2739638v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:46:17,190] [INFO] Task succeeded: Blastn
[2023-06-29 01:46:17,194] [INFO] Selected 28 target genomes.
[2023-06-29 01:46:17,195] [INFO] Target genome list was writen to GCA_027396385.1_ASM2739638v1_genomic.fna/target_genomes.txt
[2023-06-29 01:46:17,220] [INFO] Task started: fastANI
[2023-06-29 01:46:17,220] [INFO] Running command: fastANI --query /var/lib/cwl/stge9c10230-1e0c-4c73-8711-575b0d916851/GCA_027396385.1_ASM2739638v1_genomic.fna.gz --refList GCA_027396385.1_ASM2739638v1_genomic.fna/target_genomes.txt --output GCA_027396385.1_ASM2739638v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:46:43,985] [INFO] Task succeeded: fastANI
[2023-06-29 01:46:43,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:46:43,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:46:44,015] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:46:44,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 01:46:44,016] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.2179	136	702	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.206	108	702	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1431	124	702	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	75.5805	97	702	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.476	130	702	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.3811	85	702	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	75.2662	119	702	95	below_threshold
Herbidospora solisilvae	strain=NEAU-GS84	GCA_009901565.1	2696284	2696284	type	True	75.1876	115	702	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	75.1724	100	702	95	below_threshold
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	75.1642	150	702	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.1611	60	702	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	75.1532	151	702	95	below_threshold
Dietzia massiliensis	strain=Marseille-Q0999	GCA_018390595.1	2697499	2697499	type	True	75.1498	53	702	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	75.1466	79	702	95	below_threshold
Modestobacter versicolor	strain=DSM 16678	GCA_014195485.1	429133	429133	type	True	75.1381	115	702	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	75.1181	126	702	95	below_threshold
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	75.1133	124	702	95	below_threshold
Micromonospora cremea	strain=DSM 45599	GCA_900143515.1	709881	709881	type	True	75.1107	128	702	95	below_threshold
Nocardioides insulae	strain=DSM 17944	GCA_000422825.1	394734	394734	type	True	75.1096	68	702	95	below_threshold
Amycolatopsis pretoriensis	strain=NRRL B-24133	GCA_002156025.1	218821	218821	type	True	75.0515	112	702	95	below_threshold
Streptomyces tibetensis	strain=XZ 46	GCA_007655005.1	2382123	2382123	type	True	75.0386	122	702	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	75.0064	105	702	95	below_threshold
Actinosynnema mirum	strain=DSM 43827	GCA_000023245.1	40567	40567	type	True	74.9399	129	702	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.9393	94	702	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	74.8689	104	702	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	74.8079	52	702	95	below_threshold
Burkholderia glumae	strain=LMG 2196	GCA_902832765.1	337	337	type	True	74.7137	61	702	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	74.6833	61	702	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 01:46:44,018] [INFO] DFAST Taxonomy check result was written to GCA_027396385.1_ASM2739638v1_genomic.fna/tc_result.tsv
[2023-06-29 01:46:44,018] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:46:44,018] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:46:44,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference/checkm_data
[2023-06-29 01:46:44,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:46:44,051] [INFO] Task started: CheckM
[2023-06-29 01:46:44,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027396385.1_ASM2739638v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027396385.1_ASM2739638v1_genomic.fna/checkm_input GCA_027396385.1_ASM2739638v1_genomic.fna/checkm_result
[2023-06-29 01:47:17,457] [INFO] Task succeeded: CheckM
[2023-06-29 01:47:17,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:47:17,479] [INFO] ===== Completeness check finished =====
[2023-06-29 01:47:17,480] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:47:17,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027396385.1_ASM2739638v1_genomic.fna/markers.fasta)
[2023-06-29 01:47:17,480] [INFO] Task started: Blastn
[2023-06-29 01:47:17,481] [INFO] Running command: blastn -query GCA_027396385.1_ASM2739638v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg074d4a50-4030-42d7-b575-6861f9eca3bc/dqc_reference/reference_markers_gtdb.fasta -out GCA_027396385.1_ASM2739638v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:47:18,438] [INFO] Task succeeded: Blastn
[2023-06-29 01:47:18,443] [INFO] Selected 24 target genomes.
[2023-06-29 01:47:18,444] [INFO] Target genome list was writen to GCA_027396385.1_ASM2739638v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:47:18,447] [INFO] Task started: fastANI
[2023-06-29 01:47:18,447] [INFO] Running command: fastANI --query /var/lib/cwl/stge9c10230-1e0c-4c73-8711-575b0d916851/GCA_027396385.1_ASM2739638v1_genomic.fna.gz --refList GCA_027396385.1_ASM2739638v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027396385.1_ASM2739638v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:47:32,032] [INFO] Task succeeded: fastANI
[2023-06-29 01:47:32,056] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 01:47:32,057] [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_017883065.1	s__Bog-756 sp017883065	78.8744	294	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138855.1	s__Bog-756 sp003138855	78.6615	312	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.82	99.61	0.95	0.93	14	-
GCA_003153575.1	s__Bog-756 sp003153575	78.5922	238	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.41	99.41	0.75	0.75	2	-
GCA_015478655.1	s__Bog-756 sp015478655	78.3671	282	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164095.1	s__Bog-756 sp003164095	78.3285	314	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883135.1	s__Bog-756 sp017883135	78.2939	271	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883105.1	s__Bog-756 sp017883105	78.1175	179	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849265.1	s__Bog-756 sp903849265	77.9526	189	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	97.45	97.45	0.70	0.70	2	-
GCA_003157945.1	s__Bog-756 sp003157945	77.8512	179	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903894295.1	s__Bog-756 sp903894295	77.8335	195	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.67	99.55	0.93	0.92	5	-
GCA_003133325.1	s__Bog-756 sp003133325	77.7891	236	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.83	99.78	0.97	0.96	4	-
GCA_903906055.1	s__Bog-756 sp903906055	77.6258	211	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	99.06	98.82	0.85	0.81	8	-
GCA_003169235.1	s__Bog-473 sp003169235	76.8197	162	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-473	95.0	99.17	99.17	0.82	0.82	2	-
GCA_003151475.1	s__Palsa-661 sp003151475	76.7949	161	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__Palsa-661	95.0	99.35	99.14	0.89	0.86	5	-
GCA_017882995.1	s__Chersky-840 sp017882995	76.7352	146	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__Chersky-840	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002861595.1	s__GCA-2861595 sp002861595	76.6348	86	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__GCA-2861595;g__GCA-2861595	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453695.1	s__UBA8190 sp003453695	76.4431	153	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__UBA8190	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005884125.1	s__AC-35 sp005884125	76.2998	135	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-35;g__AC-35	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.1576	123	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241495.1	s__JAFAWZ01 sp019241495	76.1181	83	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__JAFAWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	75.7824	113	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_903868545.1	s__CAIPVR01 sp903868545	75.7762	117	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_016702505.1	s__JAAZBK01 sp016702505	75.7491	67	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577145.1	s__ATN2 sp003577145	75.7477	73	702	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__ATN2	95.0	99.95	99.91	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2023-06-29 01:47:32,062] [INFO] GTDB search result was written to GCA_027396385.1_ASM2739638v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:47:32,063] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:47:32,070] [INFO] DFAST_QC result json was written to GCA_027396385.1_ASM2739638v1_genomic.fna/dqc_result.json
[2023-06-29 01:47:32,070] [INFO] DFAST_QC completed!
[2023-06-29 01:47:32,070] [INFO] Total running time: 0h1m24s