[2024-01-24 13:26:11,559] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:26:11,561] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:26:11,561] [INFO] DQC Reference Directory: /var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference
[2024-01-24 13:26:12,958] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:12,959] [INFO] Task started: Prodigal
[2024-01-24 13:26:12,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg48380d30-0c29-418d-85c9-99f5373adb97/GCF_003688895.1_ASM368889v1_genomic.fna.gz | prodigal -d GCF_003688895.1_ASM368889v1_genomic.fna/cds.fna -a GCF_003688895.1_ASM368889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:26,996] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:26,997] [INFO] Task started: HMMsearch
[2024-01-24 13:26:26,997] [INFO] Running command: hmmsearch --tblout GCF_003688895.1_ASM368889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference/reference_markers.hmm GCF_003688895.1_ASM368889v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:27,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:27,293] [INFO] Found 6/6 markers.
[2024-01-24 13:26:27,334] [INFO] Query marker FASTA was written to GCF_003688895.1_ASM368889v1_genomic.fna/markers.fasta
[2024-01-24 13:26:27,335] [INFO] Task started: Blastn
[2024-01-24 13:26:27,335] [INFO] Running command: blastn -query GCF_003688895.1_ASM368889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference/reference_markers.fasta -out GCF_003688895.1_ASM368889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:27,976] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:27,980] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:27,981] [INFO] Target genome list was writen to GCF_003688895.1_ASM368889v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:27,987] [INFO] Task started: fastANI
[2024-01-24 13:26:27,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg48380d30-0c29-418d-85c9-99f5373adb97/GCF_003688895.1_ASM368889v1_genomic.fna.gz --refList GCF_003688895.1_ASM368889v1_genomic.fna/target_genomes.txt --output GCF_003688895.1_ASM368889v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:36,285] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:36,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:36,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:36,294] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:36,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:36,295] [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
Dokdonia sinensis	strain=SH27	GCA_003688895.1	2479847	2479847	type	True	100.0	1196	1199	95	conclusive
Dokdonia donghaensis	strain=DSW-1	GCA_001653755.1	326320	326320	type	True	77.9778	276	1199	95	below_threshold
Dokdonia donghaensis	strain=DSW-1	GCA_000769435.1	326320	326320	type	True	77.9172	284	1199	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	77.2515	53	1199	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	77.0517	197	1199	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	77.0238	199	1199	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	76.7364	66	1199	95	below_threshold
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	76.6006	70	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:36,297] [INFO] DFAST Taxonomy check result was written to GCF_003688895.1_ASM368889v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:36,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:36,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:36,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference/checkm_data
[2024-01-24 13:26:36,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:36,335] [INFO] Task started: CheckM
[2024-01-24 13:26:36,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688895.1_ASM368889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688895.1_ASM368889v1_genomic.fna/checkm_input GCF_003688895.1_ASM368889v1_genomic.fna/checkm_result
[2024-01-24 13:27:18,646] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:18,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:18,677] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:18,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:18,678] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688895.1_ASM368889v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:18,679] [INFO] Task started: Blastn
[2024-01-24 13:27:18,679] [INFO] Running command: blastn -query GCF_003688895.1_ASM368889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge78b8ee2-4737-4d6b-8617-d95481cd49b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688895.1_ASM368889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:19,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:19,540] [INFO] Selected 18 target genomes.
[2024-01-24 13:27:19,541] [INFO] Target genome list was writen to GCF_003688895.1_ASM368889v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:19,572] [INFO] Task started: fastANI
[2024-01-24 13:27:19,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg48380d30-0c29-418d-85c9-99f5373adb97/GCF_003688895.1_ASM368889v1_genomic.fna.gz --refList GCF_003688895.1_ASM368889v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688895.1_ASM368889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:31,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:31,883] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:31,884] [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_003688895.1	s__Dokdonia sinensis	100.0	1196	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003095655.1	s__Dokdonia sp003095655	78.143	256	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212355.1	s__Dokdonia sp000212355	78.0048	277	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_001653755.1	s__Dokdonia donghaensis	77.9765	276	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	97.85	95.71	0.96	0.91	3	-
GCA_002375495.1	s__Marinirhabdus sp002375495	77.9685	56	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_000355805.1	s__Dokdonia sp000355805	77.8368	242	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827465.1	s__Dokdonia sp007827465	77.6815	184	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685485.1	s__Formosa haliotis	77.2515	53	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011044175.1	s__Marinirhabdus sp011044175	77.1706	69	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188275.1	s__Dokdonia pacifica	77.0238	199	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009796805.1	s__Algibacter sp009796805	76.9234	50	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299525.1	s__Aquimarina sp900299525	76.6025	57	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002375695.1	s__Aequorivita sp002375695	76.4266	53	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900129745.1	s__Winogradskyella jejuensis	76.0359	58	1199	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:31,886] [INFO] GTDB search result was written to GCF_003688895.1_ASM368889v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:31,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:31,894] [INFO] DFAST_QC result json was written to GCF_003688895.1_ASM368889v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:31,894] [INFO] DFAST_QC completed!
[2024-01-24 13:27:31,894] [INFO] Total running time: 0h1m20s