[2024-01-24 13:46:01,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,203] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference
[2024-01-24 13:46:02,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,608] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg72afc3dc-284e-4fba-be44-4be6c37c0030/GCF_004358095.2_ASM435809v2_genomic.fna.gz | prodigal -d GCF_004358095.2_ASM435809v2_genomic.fna/cds.fna -a GCF_004358095.2_ASM435809v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:13,967] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:13,967] [INFO] Task started: HMMsearch
[2024-01-24 13:46:13,967] [INFO] Running command: hmmsearch --tblout GCF_004358095.2_ASM435809v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference/reference_markers.hmm GCF_004358095.2_ASM435809v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:14,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:14,300] [INFO] Found 6/6 markers.
[2024-01-24 13:46:14,328] [INFO] Query marker FASTA was written to GCF_004358095.2_ASM435809v2_genomic.fna/markers.fasta
[2024-01-24 13:46:14,328] [INFO] Task started: Blastn
[2024-01-24 13:46:14,329] [INFO] Running command: blastn -query GCF_004358095.2_ASM435809v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference/reference_markers.fasta -out GCF_004358095.2_ASM435809v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:15,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:15,008] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:15,008] [INFO] Target genome list was writen to GCF_004358095.2_ASM435809v2_genomic.fna/target_genomes.txt
[2024-01-24 13:46:15,027] [INFO] Task started: fastANI
[2024-01-24 13:46:15,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg72afc3dc-284e-4fba-be44-4be6c37c0030/GCF_004358095.2_ASM435809v2_genomic.fna.gz --refList GCF_004358095.2_ASM435809v2_genomic.fna/target_genomes.txt --output GCF_004358095.2_ASM435809v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:25,742] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:25,743] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:25,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:25,760] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:25,760] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:25,760] [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
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	86.8006	952	1158	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	79.6026	609	1158	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	79.076	487	1158	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	78.8875	441	1158	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.1394	436	1158	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.0123	380	1158	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.9865	384	1158	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.9482	353	1158	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.9149	373	1158	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.8491	361	1158	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.7411	218	1158	95	below_threshold
Aestuariibaculum sediminum	strain=TT11	GCA_014596945.1	2770637	2770637	type	True	77.6127	280	1158	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.611	202	1158	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.5951	285	1158	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.072	189	1158	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.5499	145	1158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:25,762] [INFO] DFAST Taxonomy check result was written to GCF_004358095.2_ASM435809v2_genomic.fna/tc_result.tsv
[2024-01-24 13:46:25,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:25,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:25,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference/checkm_data
[2024-01-24 13:46:25,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:25,804] [INFO] Task started: CheckM
[2024-01-24 13:46:25,805] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358095.2_ASM435809v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358095.2_ASM435809v2_genomic.fna/checkm_input GCF_004358095.2_ASM435809v2_genomic.fna/checkm_result
[2024-01-24 13:47:02,243] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:02,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,271] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:02,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:02,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358095.2_ASM435809v2_genomic.fna/markers.fasta)
[2024-01-24 13:47:02,273] [INFO] Task started: Blastn
[2024-01-24 13:47:02,273] [INFO] Running command: blastn -query GCF_004358095.2_ASM435809v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f006041-4aed-484a-8e6c-66d593278e95/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358095.2_ASM435809v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:03,273] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:03,278] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:03,278] [INFO] Target genome list was writen to GCF_004358095.2_ASM435809v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:03,316] [INFO] Task started: fastANI
[2024-01-24 13:47:03,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg72afc3dc-284e-4fba-be44-4be6c37c0030/GCF_004358095.2_ASM435809v2_genomic.fna.gz --refList GCF_004358095.2_ASM435809v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004358095.2_ASM435809v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:11,741] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:11,757] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:11,757] [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_004358095.2	s__Seonamhaeicola sp004358095	100.0	1156	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003386195.1	s__Seonamhaeicola aphaedonensis	86.8014	952	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	79.6028	609	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	79.5538	576	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	79.076	487	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.1307	437	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.0978	361	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.001	380	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.9066	374	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.2944	310	1158	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:11,759] [INFO] GTDB search result was written to GCF_004358095.2_ASM435809v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:11,760] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:11,764] [INFO] DFAST_QC result json was written to GCF_004358095.2_ASM435809v2_genomic.fna/dqc_result.json
[2024-01-24 13:47:11,764] [INFO] DFAST_QC completed!
[2024-01-24 13:47:11,765] [INFO] Total running time: 0h1m11s