[2023-06-27 19:44:54,420] [INFO] DFAST_QC pipeline started.
[2023-06-27 19:44:54,433] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 19:44:54,433] [INFO] DQC Reference Directory: /var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference
[2023-06-27 19:44:56,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 19:44:56,129] [INFO] Task started: Prodigal
[2023-06-27 19:44:56,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cc24ce8-9695-44f2-a129-a927162a9813/GCA_002384975.1_ASM238497v1_genomic.fna.gz | prodigal -d GCA_002384975.1_ASM238497v1_genomic.fna/cds.fna -a GCA_002384975.1_ASM238497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 19:45:08,853] [INFO] Task succeeded: Prodigal
[2023-06-27 19:45:08,854] [INFO] Task started: HMMsearch
[2023-06-27 19:45:08,854] [INFO] Running command: hmmsearch --tblout GCA_002384975.1_ASM238497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference/reference_markers.hmm GCA_002384975.1_ASM238497v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 19:45:09,202] [INFO] Task succeeded: HMMsearch
[2023-06-27 19:45:09,204] [INFO] Found 6/6 markers.
[2023-06-27 19:45:09,244] [INFO] Query marker FASTA was written to GCA_002384975.1_ASM238497v1_genomic.fna/markers.fasta
[2023-06-27 19:45:09,244] [INFO] Task started: Blastn
[2023-06-27 19:45:09,244] [INFO] Running command: blastn -query GCA_002384975.1_ASM238497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference/reference_markers.fasta -out GCA_002384975.1_ASM238497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:45:10,167] [INFO] Task succeeded: Blastn
[2023-06-27 19:45:10,172] [INFO] Selected 21 target genomes.
[2023-06-27 19:45:10,173] [INFO] Target genome list was writen to GCA_002384975.1_ASM238497v1_genomic.fna/target_genomes.txt
[2023-06-27 19:45:10,177] [INFO] Task started: fastANI
[2023-06-27 19:45:10,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cc24ce8-9695-44f2-a129-a927162a9813/GCA_002384975.1_ASM238497v1_genomic.fna.gz --refList GCA_002384975.1_ASM238497v1_genomic.fna/target_genomes.txt --output GCA_002384975.1_ASM238497v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 19:45:27,902] [INFO] Task succeeded: fastANI
[2023-06-27 19:45:27,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 19:45:27,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 19:45:27,918] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 19:45:27,919] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 19:45:27,919] [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
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	83.2123	966	1359	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	83.1827	947	1359	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	83.1263	982	1359	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	82.5414	869	1359	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.2096	434	1359	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.9947	332	1359	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.8828	401	1359	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	77.7665	389	1359	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.7393	341	1359	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.6805	235	1359	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.6359	330	1359	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.5184	277	1359	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.4576	295	1359	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.2608	257	1359	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.2289	265	1359	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.942	217	1359	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	76.3085	75	1359	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	74.7455	88	1359	95	below_threshold
Actinopolymorpha pittospori	strain=DSM 45354	GCA_014873875.1	648752	648752	type	True	74.5973	68	1359	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 19:45:27,921] [INFO] DFAST Taxonomy check result was written to GCA_002384975.1_ASM238497v1_genomic.fna/tc_result.tsv
[2023-06-27 19:45:27,921] [INFO] ===== Taxonomy check completed =====
[2023-06-27 19:45:27,922] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 19:45:27,922] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference/checkm_data
[2023-06-27 19:45:27,923] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 19:45:27,965] [INFO] Task started: CheckM
[2023-06-27 19:45:27,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002384975.1_ASM238497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002384975.1_ASM238497v1_genomic.fna/checkm_input GCA_002384975.1_ASM238497v1_genomic.fna/checkm_result
[2023-06-27 19:46:09,166] [INFO] Task succeeded: CheckM
[2023-06-27 19:46:09,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.76%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 19:46:09,198] [INFO] ===== Completeness check finished =====
[2023-06-27 19:46:09,198] [INFO] ===== Start GTDB Search =====
[2023-06-27 19:46:09,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002384975.1_ASM238497v1_genomic.fna/markers.fasta)
[2023-06-27 19:46:09,199] [INFO] Task started: Blastn
[2023-06-27 19:46:09,199] [INFO] Running command: blastn -query GCA_002384975.1_ASM238497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33ef5b42-f186-404f-9b66-7c750db12f8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_002384975.1_ASM238497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:46:10,518] [INFO] Task succeeded: Blastn
[2023-06-27 19:46:10,523] [INFO] Selected 13 target genomes.
[2023-06-27 19:46:10,523] [INFO] Target genome list was writen to GCA_002384975.1_ASM238497v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 19:46:10,529] [INFO] Task started: fastANI
[2023-06-27 19:46:10,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cc24ce8-9695-44f2-a129-a927162a9813/GCA_002384975.1_ASM238497v1_genomic.fna.gz --refList GCA_002384975.1_ASM238497v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002384975.1_ASM238497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 19:46:19,736] [INFO] Task succeeded: fastANI
[2023-06-27 19:46:19,751] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 19:46:19,752] [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_002695005.1	s__Maritimibacter sp002695005	99.9751	1347	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000152805.1	s__Maritimibacter alkaliphilus	83.1351	981	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	97.94	96.90	0.93	0.88	4	-
GCF_009882975.1	s__Maritimibacter harenae	82.5569	867	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218265.1	s__Maritimibacter sp019218265	80.3389	658	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019218295.1	s__Maritimibacter sp019218295	80.1204	650	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003520545.1	s__Maritimibacter sp003520545	79.9252	511	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389895.1	s__Maritimibacter sp011389895	79.3519	586	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	79.0368	519	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.2495	258	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	76.3085	75	1359	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424625.1	s__Baekduia woesei_A	75.1101	89	1359	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 19:46:19,754] [INFO] GTDB search result was written to GCA_002384975.1_ASM238497v1_genomic.fna/result_gtdb.tsv
[2023-06-27 19:46:19,754] [INFO] ===== GTDB Search completed =====
[2023-06-27 19:46:19,760] [INFO] DFAST_QC result json was written to GCA_002384975.1_ASM238497v1_genomic.fna/dqc_result.json
[2023-06-27 19:46:19,760] [INFO] DFAST_QC completed!
[2023-06-27 19:46:19,760] [INFO] Total running time: 0h1m25s