[2023-06-19 13:14:07,504] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:07,509] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:07,509] [INFO] DQC Reference Directory: /var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference
[2023-06-19 13:14:09,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:09,014] [INFO] Task started: Prodigal
[2023-06-19 13:14:09,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg3746c4bf-88bf-4f6c-987d-c2a4985305cf/GCA_013698095.1_ASM1369809v1_genomic.fna.gz | prodigal -d GCA_013698095.1_ASM1369809v1_genomic.fna/cds.fna -a GCA_013698095.1_ASM1369809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:18,502] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:18,502] [INFO] Task started: HMMsearch
[2023-06-19 13:14:18,502] [INFO] Running command: hmmsearch --tblout GCA_013698095.1_ASM1369809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference/reference_markers.hmm GCA_013698095.1_ASM1369809v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:18,819] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:18,820] [INFO] Found 6/6 markers.
[2023-06-19 13:14:18,873] [INFO] Query marker FASTA was written to GCA_013698095.1_ASM1369809v1_genomic.fna/markers.fasta
[2023-06-19 13:14:18,873] [INFO] Task started: Blastn
[2023-06-19 13:14:18,873] [INFO] Running command: blastn -query GCA_013698095.1_ASM1369809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference/reference_markers.fasta -out GCA_013698095.1_ASM1369809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:19,585] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:19,589] [INFO] Selected 20 target genomes.
[2023-06-19 13:14:19,590] [INFO] Target genome list was writen to GCA_013698095.1_ASM1369809v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:19,592] [INFO] Task started: fastANI
[2023-06-19 13:14:19,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg3746c4bf-88bf-4f6c-987d-c2a4985305cf/GCA_013698095.1_ASM1369809v1_genomic.fna.gz --refList GCA_013698095.1_ASM1369809v1_genomic.fna/target_genomes.txt --output GCA_013698095.1_ASM1369809v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:14:37,260] [INFO] Task succeeded: fastANI
[2023-06-19 13:14:37,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:14:37,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:14:37,272] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:14:37,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:14:37,273] [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
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	75.146	73	1173	95	below_threshold
Longispora albida	strain=DSM 44784	GCA_000379825.1	203523	203523	type	True	74.981	97	1173	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	74.971	77	1173	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.9577	137	1173	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.9533	80	1173	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	74.9093	108	1173	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	74.9005	50	1173	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	74.8966	135	1173	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	74.8948	133	1173	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	74.815	142	1173	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	74.796	152	1173	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	74.667	53	1173	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	74.6667	59	1173	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:14:37,276] [INFO] DFAST Taxonomy check result was written to GCA_013698095.1_ASM1369809v1_genomic.fna/tc_result.tsv
[2023-06-19 13:14:37,276] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:14:37,277] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:14:37,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference/checkm_data
[2023-06-19 13:14:37,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:14:37,327] [INFO] Task started: CheckM
[2023-06-19 13:14:37,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013698095.1_ASM1369809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013698095.1_ASM1369809v1_genomic.fna/checkm_input GCA_013698095.1_ASM1369809v1_genomic.fna/checkm_result
[2023-06-19 13:15:21,475] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:21,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:21,499] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:21,499] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:21,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013698095.1_ASM1369809v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:21,500] [INFO] Task started: Blastn
[2023-06-19 13:15:21,500] [INFO] Running command: blastn -query GCA_013698095.1_ASM1369809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc217ff7c-2940-4162-b630-e5fe8797a944/dqc_reference/reference_markers_gtdb.fasta -out GCA_013698095.1_ASM1369809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:22,490] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:22,495] [INFO] Selected 14 target genomes.
[2023-06-19 13:15:22,495] [INFO] Target genome list was writen to GCA_013698095.1_ASM1369809v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:22,497] [INFO] Task started: fastANI
[2023-06-19 13:15:22,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg3746c4bf-88bf-4f6c-987d-c2a4985305cf/GCA_013698095.1_ASM1369809v1_genomic.fna.gz --refList GCA_013698095.1_ASM1369809v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013698095.1_ASM1369809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:15:30,612] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:30,624] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:15:30,624] [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_013698095.1	s__CF-46 sp013698095	99.9999	1165	1173	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	conclusive
GCA_013695505.1	s__CF-46 sp013695505	81.3446	368	1173	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_005882635.1	s__CF-46 sp005882635	80.9623	542	1173	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_016191345.1	s__UBA5189 sp016191345	78.9503	326	1173	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_001795245.1	s__UBA5189 sp001795245	78.7683	333	1173	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	78.7118	368	1173	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	78.6709	257	1173	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	78.4226	238	1173	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_016200745.1	s__SPCO01 sp016200745	78.3897	275	1173	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__SPCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695255.1	s__JACDAV01 sp013695255	78.2748	265	1173	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__JACDAV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881905.1	s__Chersky-267 sp017881905	78.2495	293	1173	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Chersky-267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017881915.1	s__Palsa-1033 sp017881915	78.1958	284	1173	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__Palsa-1033	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698385.1	s__SPCO01 sp013698385	77.9338	198	1173	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__SPCO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822495.1	s__CAIJPD01 sp903822495	77.6903	243	1173	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CAIJPD01	95.0	99.94	99.94	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-19 13:15:30,630] [INFO] GTDB search result was written to GCA_013698095.1_ASM1369809v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:15:30,631] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:15:30,634] [INFO] DFAST_QC result json was written to GCA_013698095.1_ASM1369809v1_genomic.fna/dqc_result.json
[2023-06-19 13:15:30,634] [INFO] DFAST_QC completed!
[2023-06-19 13:15:30,634] [INFO] Total running time: 0h1m23s