[2024-01-24 12:15:03,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:03,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:03,785] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference
[2024-01-24 12:15:05,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,112] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,113] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e5f796c-26b3-446d-9fc8-7aca268a2e0c/GCF_021532625.1_ASM2153262v1_genomic.fna.gz | prodigal -d GCF_021532625.1_ASM2153262v1_genomic.fna/cds.fna -a GCF_021532625.1_ASM2153262v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:16,232] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:16,233] [INFO] Task started: HMMsearch
[2024-01-24 12:15:16,233] [INFO] Running command: hmmsearch --tblout GCF_021532625.1_ASM2153262v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference/reference_markers.hmm GCF_021532625.1_ASM2153262v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:16,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:16,503] [INFO] Found 6/6 markers.
[2024-01-24 12:15:16,539] [INFO] Query marker FASTA was written to GCF_021532625.1_ASM2153262v1_genomic.fna/markers.fasta
[2024-01-24 12:15:16,539] [INFO] Task started: Blastn
[2024-01-24 12:15:16,539] [INFO] Running command: blastn -query GCF_021532625.1_ASM2153262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference/reference_markers.fasta -out GCF_021532625.1_ASM2153262v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:17,248] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:17,251] [INFO] Selected 17 target genomes.
[2024-01-24 12:15:17,252] [INFO] Target genome list was writen to GCF_021532625.1_ASM2153262v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:17,260] [INFO] Task started: fastANI
[2024-01-24 12:15:17,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e5f796c-26b3-446d-9fc8-7aca268a2e0c/GCF_021532625.1_ASM2153262v1_genomic.fna.gz --refList GCF_021532625.1_ASM2153262v1_genomic.fna/target_genomes.txt --output GCF_021532625.1_ASM2153262v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:29,451] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:29,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:29,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:29,470] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:29,470] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:29,470] [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
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	79.6134	470	1147	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	79.5319	482	1147	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	79.3008	444	1147	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	77.9953	341	1147	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	77.6346	340	1147	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.508	267	1147	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	77.5046	159	1147	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	77.4705	292	1147	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.1045	103	1147	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.7819	99	1147	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.7612	88	1147	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	76.5333	87	1147	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.3434	81	1147	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.1562	85	1147	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	75.9005	75	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:29,472] [INFO] DFAST Taxonomy check result was written to GCF_021532625.1_ASM2153262v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:29,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:29,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:29,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference/checkm_data
[2024-01-24 12:15:29,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:29,515] [INFO] Task started: CheckM
[2024-01-24 12:15:29,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021532625.1_ASM2153262v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021532625.1_ASM2153262v1_genomic.fna/checkm_input GCF_021532625.1_ASM2153262v1_genomic.fna/checkm_result
[2024-01-24 12:16:05,575] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:05,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:05,598] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:05,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:05,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021532625.1_ASM2153262v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:05,599] [INFO] Task started: Blastn
[2024-01-24 12:16:05,599] [INFO] Running command: blastn -query GCF_021532625.1_ASM2153262v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa7d14b2-f41c-4ffb-a3c6-c534c58835a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_021532625.1_ASM2153262v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:06,487] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:06,492] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:06,492] [INFO] Target genome list was writen to GCF_021532625.1_ASM2153262v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:06,503] [INFO] Task started: fastANI
[2024-01-24 12:16:06,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e5f796c-26b3-446d-9fc8-7aca268a2e0c/GCF_021532625.1_ASM2153262v1_genomic.fna.gz --refList GCF_021532625.1_ASM2153262v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021532625.1_ASM2153262v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:15,991] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:16,010] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:16,010] [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_018861045.1	s__Octadecabacter sp018861045	89.5737	946	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	79.5319	482	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	79.3008	444	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	78.3715	313	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCA_018500005.1	s__Octadecabacter sp018500005	78.3145	310	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886375.1	s__Octadecabacter sp017886375	78.0384	338	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155735.2	s__Octadecabacter arcticus	77.9953	341	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCA_003533975.1	s__Octadecabacter sp003533975	77.8473	289	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155675.2	s__Octadecabacter antarcticus	77.6324	341	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	77.508	267	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172275.1	s__Pseudooctadecabacter jejudonensis	77.4705	292	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooctadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	77.4205	160	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065155.1	s__SW4 sp002732825	76.6754	219	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SW4	95.0	98.61	98.61	0.85	0.85	2	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	76.5224	86	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_002210095.1	s__Marinibacterium profundimaris	76.111	78	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:16,011] [INFO] GTDB search result was written to GCF_021532625.1_ASM2153262v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:16,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:16,016] [INFO] DFAST_QC result json was written to GCF_021532625.1_ASM2153262v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:16,017] [INFO] DFAST_QC completed!
[2024-01-24 12:16:16,017] [INFO] Total running time: 0h1m12s