[2023-06-30 05:03:47,259] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:03:47,262] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:03:47,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference
[2023-06-30 05:03:48,662] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:03:48,663] [INFO] Task started: Prodigal
[2023-06-30 05:03:48,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg5be51eee-4442-42ea-bc77-3502bf477ad2/GCA_024685845.1_ASM2468584v1_genomic.fna.gz | prodigal -d GCA_024685845.1_ASM2468584v1_genomic.fna/cds.fna -a GCA_024685845.1_ASM2468584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:03:55,198] [INFO] Task succeeded: Prodigal
[2023-06-30 05:03:55,198] [INFO] Task started: HMMsearch
[2023-06-30 05:03:55,198] [INFO] Running command: hmmsearch --tblout GCA_024685845.1_ASM2468584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference/reference_markers.hmm GCA_024685845.1_ASM2468584v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:03:55,441] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:03:55,443] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5be51eee-4442-42ea-bc77-3502bf477ad2/GCA_024685845.1_ASM2468584v1_genomic.fna.gz]
[2023-06-30 05:03:55,477] [INFO] Query marker FASTA was written to GCA_024685845.1_ASM2468584v1_genomic.fna/markers.fasta
[2023-06-30 05:03:55,477] [INFO] Task started: Blastn
[2023-06-30 05:03:55,477] [INFO] Running command: blastn -query GCA_024685845.1_ASM2468584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference/reference_markers.fasta -out GCA_024685845.1_ASM2468584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:03:56,124] [INFO] Task succeeded: Blastn
[2023-06-30 05:03:56,128] [INFO] Selected 26 target genomes.
[2023-06-30 05:03:56,128] [INFO] Target genome list was writen to GCA_024685845.1_ASM2468584v1_genomic.fna/target_genomes.txt
[2023-06-30 05:03:56,130] [INFO] Task started: fastANI
[2023-06-30 05:03:56,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be51eee-4442-42ea-bc77-3502bf477ad2/GCA_024685845.1_ASM2468584v1_genomic.fna.gz --refList GCA_024685845.1_ASM2468584v1_genomic.fna/target_genomes.txt --output GCA_024685845.1_ASM2468584v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:04:11,253] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:11,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:04:11,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:04:11,268] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:04:11,268] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:04:11,269] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	77.6736	145	667	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.9304	87	667	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	76.9034	94	667	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.7242	106	667	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.6931	106	667	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3576	87	667	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3153	89	667	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	76.2849	68	667	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.2262	54	667	95	below_threshold
Roseobacter litoralis	strain=Och 149	GCA_000154785.2	42443	42443	type	True	76.2159	63	667	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.1585	62	667	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_002796795.1	1156985	1156985	type	True	76.0635	56	667	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	76.0188	56	667	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.9807	57	667	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	75.9807	57	667	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	75.9443	55	667	95	below_threshold
Actibacterium pelagium	strain=JN33	GCA_002285415.1	2029103	2029103	type	True	75.6609	50	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:04:11,271] [INFO] DFAST Taxonomy check result was written to GCA_024685845.1_ASM2468584v1_genomic.fna/tc_result.tsv
[2023-06-30 05:04:11,271] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:04:11,271] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:04:11,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference/checkm_data
[2023-06-30 05:04:11,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:04:11,303] [INFO] Task started: CheckM
[2023-06-30 05:04:11,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024685845.1_ASM2468584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024685845.1_ASM2468584v1_genomic.fna/checkm_input GCA_024685845.1_ASM2468584v1_genomic.fna/checkm_result
[2023-06-30 05:04:36,833] [INFO] Task succeeded: CheckM
[2023-06-30 05:04:36,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.74%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:04:36,861] [INFO] ===== Completeness check finished =====
[2023-06-30 05:04:36,862] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:04:36,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024685845.1_ASM2468584v1_genomic.fna/markers.fasta)
[2023-06-30 05:04:36,863] [INFO] Task started: Blastn
[2023-06-30 05:04:36,863] [INFO] Running command: blastn -query GCA_024685845.1_ASM2468584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31433a8a-e485-4a8a-9ec8-d0bfea43b1f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_024685845.1_ASM2468584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:04:37,790] [INFO] Task succeeded: Blastn
[2023-06-30 05:04:37,794] [INFO] Selected 14 target genomes.
[2023-06-30 05:04:37,795] [INFO] Target genome list was writen to GCA_024685845.1_ASM2468584v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:04:37,800] [INFO] Task started: fastANI
[2023-06-30 05:04:37,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be51eee-4442-42ea-bc77-3502bf477ad2/GCA_024685845.1_ASM2468584v1_genomic.fna.gz --refList GCA_024685845.1_ASM2468584v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024685845.1_ASM2468584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:04:45,900] [INFO] Task succeeded: fastANI
[2023-06-30 05:04:45,919] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 05:04:45,919] [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_002478745.1	s__Ascidiaceihabitans sp002478745	94.9971	519	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	-
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	92.6248	305	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182105.1	s__Ascidiaceihabitans sp905182105	90.2996	463	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182355.1	s__Ascidiaceihabitans sp905182355	79.2087	259	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	77.6736	145	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	76.8285	87	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.7242	106	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.3153	89	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_900102795.1	s__Epibacterium ulvae	76.0188	56	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001458415.1	s__Epibacterium multivorans	75.9807	57	667	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-30 05:04:45,922] [INFO] GTDB search result was written to GCA_024685845.1_ASM2468584v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:04:45,922] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:04:45,927] [INFO] DFAST_QC result json was written to GCA_024685845.1_ASM2468584v1_genomic.fna/dqc_result.json
[2023-06-30 05:04:45,927] [INFO] DFAST_QC completed!
[2023-06-30 05:04:45,927] [INFO] Total running time: 0h0m59s