[2024-01-24 13:37:05,148] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,150] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference
[2024-01-24 13:37:06,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,650] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,650] [INFO] Running command: gunzip -c /var/lib/cwl/stgb68d66d5-3767-46d1-abd3-660cd3127a98/GCF_013346665.1_ASM1334666v1_genomic.fna.gz | prodigal -d GCF_013346665.1_ASM1334666v1_genomic.fna/cds.fna -a GCF_013346665.1_ASM1334666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:19,409] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:19,409] [INFO] Task started: HMMsearch
[2024-01-24 13:37:19,409] [INFO] Running command: hmmsearch --tblout GCF_013346665.1_ASM1334666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference/reference_markers.hmm GCF_013346665.1_ASM1334666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:19,702] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:19,703] [INFO] Found 6/6 markers.
[2024-01-24 13:37:19,755] [INFO] Query marker FASTA was written to GCF_013346665.1_ASM1334666v1_genomic.fna/markers.fasta
[2024-01-24 13:37:19,756] [INFO] Task started: Blastn
[2024-01-24 13:37:19,756] [INFO] Running command: blastn -query GCF_013346665.1_ASM1334666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference/reference_markers.fasta -out GCF_013346665.1_ASM1334666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:20,575] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:20,578] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:20,578] [INFO] Target genome list was writen to GCF_013346665.1_ASM1334666v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:20,583] [INFO] Task started: fastANI
[2024-01-24 13:37:20,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68d66d5-3767-46d1-abd3-660cd3127a98/GCF_013346665.1_ASM1334666v1_genomic.fna.gz --refList GCF_013346665.1_ASM1334666v1_genomic.fna/target_genomes.txt --output GCF_013346665.1_ASM1334666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:30,544] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:30,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:30,545] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:30,557] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:30,557] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:30,557] [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
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	100.0	1230	1247	95	conclusive
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	85.4015	891	1247	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	84.0402	810	1247	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	84.0301	842	1247	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	84.0035	834	1247	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	78.1061	317	1247	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	78.0104	317	1247	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.9529	265	1247	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.8739	402	1247	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.5305	259	1247	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.9217	263	1247	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.9126	149	1247	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.4483	216	1247	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:30,559] [INFO] DFAST Taxonomy check result was written to GCF_013346665.1_ASM1334666v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:30,560] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:30,560] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:30,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference/checkm_data
[2024-01-24 13:37:30,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:30,600] [INFO] Task started: CheckM
[2024-01-24 13:37:30,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013346665.1_ASM1334666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013346665.1_ASM1334666v1_genomic.fna/checkm_input GCF_013346665.1_ASM1334666v1_genomic.fna/checkm_result
[2024-01-24 13:38:11,034] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:11,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:11,060] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:11,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:11,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013346665.1_ASM1334666v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:11,061] [INFO] Task started: Blastn
[2024-01-24 13:38:11,061] [INFO] Running command: blastn -query GCF_013346665.1_ASM1334666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3de7064-ed32-4678-943a-1a4268d0e0d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_013346665.1_ASM1334666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:12,310] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:12,318] [INFO] Selected 11 target genomes.
[2024-01-24 13:38:12,318] [INFO] Target genome list was writen to GCF_013346665.1_ASM1334666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:12,332] [INFO] Task started: fastANI
[2024-01-24 13:38:12,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68d66d5-3767-46d1-abd3-660cd3127a98/GCF_013346665.1_ASM1334666v1_genomic.fna.gz --refList GCF_013346665.1_ASM1334666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013346665.1_ASM1334666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:21,473] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:21,487] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:21,487] [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
GCF_013346665.1	s__Sulfitobacter maritimus	100.0	1226	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900102535.1	s__Sulfitobacter delicatus	85.3979	891	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	84.5749	827	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_017743885.1	s__Sulfitobacter sp001635605	84.3109	805	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_000172095.1	s__Sulfitobacter indolifex	84.0417	828	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	84.0284	811	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCA_002703405.1	s__Sulfitobacter sp002703405	83.7374	687	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.87	96.48	0.79	0.78	3	-
GCF_003335585.1	s__Sulfitobacter sp003335585	79.2844	528	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	78.044	316	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.9195	404	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014899185.1	s__Pseudooceanicola antarcticus_A	77.5305	259	1247	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:21,489] [INFO] GTDB search result was written to GCF_013346665.1_ASM1334666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:21,489] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:21,492] [INFO] DFAST_QC result json was written to GCF_013346665.1_ASM1334666v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:21,493] [INFO] DFAST_QC completed!
[2024-01-24 13:38:21,493] [INFO] Total running time: 0h1m16s