[2023-06-30 11:36:12,142] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:36:12,144] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:36:12,145] [INFO] DQC Reference Directory: /var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference
[2023-06-30 11:36:13,313] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:36:13,314] [INFO] Task started: Prodigal
[2023-06-30 11:36:13,314] [INFO] Running command: gunzip -c /var/lib/cwl/stg2a0e697e-4419-40c1-b6ce-804b112f20ac/GCA_024635735.1_ASM2463573v1_genomic.fna.gz | prodigal -d GCA_024635735.1_ASM2463573v1_genomic.fna/cds.fna -a GCA_024635735.1_ASM2463573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:36:21,469] [INFO] Task succeeded: Prodigal
[2023-06-30 11:36:21,470] [INFO] Task started: HMMsearch
[2023-06-30 11:36:21,470] [INFO] Running command: hmmsearch --tblout GCA_024635735.1_ASM2463573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference/reference_markers.hmm GCA_024635735.1_ASM2463573v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:36:21,654] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:36:21,655] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2a0e697e-4419-40c1-b6ce-804b112f20ac/GCA_024635735.1_ASM2463573v1_genomic.fna.gz]
[2023-06-30 11:36:21,679] [INFO] Query marker FASTA was written to GCA_024635735.1_ASM2463573v1_genomic.fna/markers.fasta
[2023-06-30 11:36:21,679] [INFO] Task started: Blastn
[2023-06-30 11:36:21,679] [INFO] Running command: blastn -query GCA_024635735.1_ASM2463573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference/reference_markers.fasta -out GCA_024635735.1_ASM2463573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:22,281] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:22,285] [INFO] Selected 16 target genomes.
[2023-06-30 11:36:22,285] [INFO] Target genome list was writen to GCA_024635735.1_ASM2463573v1_genomic.fna/target_genomes.txt
[2023-06-30 11:36:22,315] [INFO] Task started: fastANI
[2023-06-30 11:36:22,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a0e697e-4419-40c1-b6ce-804b112f20ac/GCA_024635735.1_ASM2463573v1_genomic.fna.gz --refList GCA_024635735.1_ASM2463573v1_genomic.fna/target_genomes.txt --output GCA_024635735.1_ASM2463573v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:36:31,439] [INFO] Task succeeded: fastANI
[2023-06-30 11:36:31,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:36:31,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:36:31,453] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:36:31,453] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 11:36:31,454] [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
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	78.9887	298	735	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.8759	317	735	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	78.7883	291	735	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	78.6727	249	735	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	78.6527	223	735	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	78.5947	291	735	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	78.5719	288	735	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	78.5682	253	735	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	78.5669	244	735	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.1283	141	735	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	76.9748	103	735	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.9733	154	735	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	76.6764	94	735	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	75.8314	56	735	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:36:31,456] [INFO] DFAST Taxonomy check result was written to GCA_024635735.1_ASM2463573v1_genomic.fna/tc_result.tsv
[2023-06-30 11:36:31,456] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:36:31,457] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:36:31,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference/checkm_data
[2023-06-30 11:36:31,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:36:31,487] [INFO] Task started: CheckM
[2023-06-30 11:36:31,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024635735.1_ASM2463573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024635735.1_ASM2463573v1_genomic.fna/checkm_input GCA_024635735.1_ASM2463573v1_genomic.fna/checkm_result
[2023-06-30 11:37:00,069] [INFO] Task succeeded: CheckM
[2023-06-30 11:37:00,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:37:00,087] [INFO] ===== Completeness check finished =====
[2023-06-30 11:37:00,088] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:37:00,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024635735.1_ASM2463573v1_genomic.fna/markers.fasta)
[2023-06-30 11:37:00,088] [INFO] Task started: Blastn
[2023-06-30 11:37:00,088] [INFO] Running command: blastn -query GCA_024635735.1_ASM2463573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9e07141-f39c-4b9c-bf1b-7a3121305d4f/dqc_reference/reference_markers_gtdb.fasta -out GCA_024635735.1_ASM2463573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:37:00,922] [INFO] Task succeeded: Blastn
[2023-06-30 11:37:00,926] [INFO] Selected 16 target genomes.
[2023-06-30 11:37:00,926] [INFO] Target genome list was writen to GCA_024635735.1_ASM2463573v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:37:00,955] [INFO] Task started: fastANI
[2023-06-30 11:37:00,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a0e697e-4419-40c1-b6ce-804b112f20ac/GCA_024635735.1_ASM2463573v1_genomic.fna.gz --refList GCA_024635735.1_ASM2463573v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024635735.1_ASM2463573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:37:10,274] [INFO] Task succeeded: fastANI
[2023-06-30 11:37:10,287] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 11:37:10,288] [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_003054225.1	s__Gramella gaetbulicola	78.9887	298	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105135.1	s__Gramella sp900105135	78.8854	274	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	78.7883	291	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_001889005.1	s__Gramella salexigens	78.6527	223	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	78.6083	290	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004332155.1	s__Gramella sp004332155	78.6062	258	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	78.5669	244	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024155.1	s__Gramella fulva	78.3121	264	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735695.1	s__Gramella sp009735695	78.0071	233	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006714895.1	s__Gramella sp006714895	77.6979	195	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	77.1504	124	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112105.1	s__Zunongwangia mangrovi	76.7646	112	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129445.1	s__Salegentibacter echinorum	76.6764	94	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403785.1	s__Gillisia sp000403785	76.6498	87	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104765.1	s__Gillisia sp900104765	76.2546	92	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_902499555.1	s__Mesonia oceanica	75.8314	56	735	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
--------------------------------------------------------------------------------
[2023-06-30 11:37:10,290] [INFO] GTDB search result was written to GCA_024635735.1_ASM2463573v1_genomic.fna/result_gtdb.tsv
[2023-06-30 11:37:10,291] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:37:10,295] [INFO] DFAST_QC result json was written to GCA_024635735.1_ASM2463573v1_genomic.fna/dqc_result.json
[2023-06-30 11:37:10,295] [INFO] DFAST_QC completed!
[2023-06-30 11:37:10,295] [INFO] Total running time: 0h0m58s