[2024-01-24 11:35:11,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference
[2024-01-24 11:35:12,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,983] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,984] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c101fce-a869-4166-9cfe-2237ec2d0205/GCF_014764305.1_ASM1476430v1_genomic.fna.gz | prodigal -d GCF_014764305.1_ASM1476430v1_genomic.fna/cds.fna -a GCF_014764305.1_ASM1476430v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:21,490] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:21,490] [INFO] Task started: HMMsearch
[2024-01-24 11:35:21,490] [INFO] Running command: hmmsearch --tblout GCF_014764305.1_ASM1476430v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference/reference_markers.hmm GCF_014764305.1_ASM1476430v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:21,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:21,814] [INFO] Found 6/6 markers.
[2024-01-24 11:35:21,842] [INFO] Query marker FASTA was written to GCF_014764305.1_ASM1476430v1_genomic.fna/markers.fasta
[2024-01-24 11:35:21,842] [INFO] Task started: Blastn
[2024-01-24 11:35:21,842] [INFO] Running command: blastn -query GCF_014764305.1_ASM1476430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference/reference_markers.fasta -out GCF_014764305.1_ASM1476430v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:22,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:22,549] [INFO] Selected 12 target genomes.
[2024-01-24 11:35:22,550] [INFO] Target genome list was writen to GCF_014764305.1_ASM1476430v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:22,555] [INFO] Task started: fastANI
[2024-01-24 11:35:22,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c101fce-a869-4166-9cfe-2237ec2d0205/GCF_014764305.1_ASM1476430v1_genomic.fna.gz --refList GCF_014764305.1_ASM1476430v1_genomic.fna/target_genomes.txt --output GCF_014764305.1_ASM1476430v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:31,127] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:31,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:31,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:31,139] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:31,140] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:31,140] [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
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	100.0	1028	1029	95	conclusive
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	86.6808	771	1029	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	86.6675	763	1029	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	86.5215	769	1029	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	79.6828	540	1029	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	79.3527	550	1029	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	78.6036	496	1029	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	78.1259	245	1029	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	77.7581	249	1029	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.7581	263	1029	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.6205	233	1029	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.5978	230	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:31,141] [INFO] DFAST Taxonomy check result was written to GCF_014764305.1_ASM1476430v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:31,142] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:31,142] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:31,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference/checkm_data
[2024-01-24 11:35:31,144] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:31,180] [INFO] Task started: CheckM
[2024-01-24 11:35:31,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014764305.1_ASM1476430v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014764305.1_ASM1476430v1_genomic.fna/checkm_input GCF_014764305.1_ASM1476430v1_genomic.fna/checkm_result
[2024-01-24 11:36:01,831] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:01,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,855] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:01,855] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:01,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014764305.1_ASM1476430v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:01,856] [INFO] Task started: Blastn
[2024-01-24 11:36:01,856] [INFO] Running command: blastn -query GCF_014764305.1_ASM1476430v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d12631-880d-4c47-91f5-0ae9ace0cebd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014764305.1_ASM1476430v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:02,798] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:02,803] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:02,803] [INFO] Target genome list was writen to GCF_014764305.1_ASM1476430v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:02,813] [INFO] Task started: fastANI
[2024-01-24 11:36:02,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c101fce-a869-4166-9cfe-2237ec2d0205/GCF_014764305.1_ASM1476430v1_genomic.fna.gz --refList GCF_014764305.1_ASM1476430v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014764305.1_ASM1476430v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:12,263] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,275] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:12,275] [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_014764305.1	s__Mesoflavibacter profundi	100.0	1028	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	conclusive
GCF_000422365.1	s__Mesoflavibacter zeaxanthinifaciens	86.6711	770	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	97.07	97.05	0.91	0.91	3	-
GCF_003259525.1	s__Olleya aquimaris	79.7112	537	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785945.1	s__Olleya sediminilitoris	79.4454	552	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.16	97.66	0.93	0.91	5	-
GCF_000518485.1	s__Olleya marilimosa	79.3442	551	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	97.58	97.25	0.92	0.89	4	-
GCF_007827365.1	s__Olleya sp002323495	79.0323	544	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	78.8933	477	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	78.8688	433	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	78.8605	457	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114005.1	s__Olleya namhaensis	78.6154	494	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	98.20	98.20	0.94	0.94	2	-
GCF_004843725.1	s__Olleya sp004843725	78.6043	477	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831645.1	s__Olleya sp002831645	78.5592	469	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	77.7975	361	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,277] [INFO] GTDB search result was written to GCF_014764305.1_ASM1476430v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:12,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:12,283] [INFO] DFAST_QC result json was written to GCF_014764305.1_ASM1476430v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:12,283] [INFO] DFAST_QC completed!
[2024-01-24 11:36:12,284] [INFO] Total running time: 0h1m1s