[2024-01-24 11:27:04,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,882] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,883] [INFO] DQC Reference Directory: /var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference
[2024-01-24 11:27:06,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:06,117] [INFO] Task started: Prodigal
[2024-01-24 11:27:06,117] [INFO] Running command: gunzip -c /var/lib/cwl/stg9868d03e-ede7-41cc-ad75-fb0e4d79dcd7/GCF_003576475.1_ASM357647v1_genomic.fna.gz | prodigal -d GCF_003576475.1_ASM357647v1_genomic.fna/cds.fna -a GCF_003576475.1_ASM357647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:35,947] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:35,948] [INFO] Task started: HMMsearch
[2024-01-24 11:27:35,948] [INFO] Running command: hmmsearch --tblout GCF_003576475.1_ASM357647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference/reference_markers.hmm GCF_003576475.1_ASM357647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:36,270] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:36,271] [INFO] Found 6/6 markers.
[2024-01-24 11:27:36,321] [INFO] Query marker FASTA was written to GCF_003576475.1_ASM357647v1_genomic.fna/markers.fasta
[2024-01-24 11:27:36,322] [INFO] Task started: Blastn
[2024-01-24 11:27:36,322] [INFO] Running command: blastn -query GCF_003576475.1_ASM357647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference/reference_markers.fasta -out GCF_003576475.1_ASM357647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:36,937] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:36,941] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:36,942] [INFO] Target genome list was writen to GCF_003576475.1_ASM357647v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:36,952] [INFO] Task started: fastANI
[2024-01-24 11:27:36,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg9868d03e-ede7-41cc-ad75-fb0e4d79dcd7/GCF_003576475.1_ASM357647v1_genomic.fna.gz --refList GCF_003576475.1_ASM357647v1_genomic.fna/target_genomes.txt --output GCF_003576475.1_ASM357647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:53,380] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:53,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:53,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:53,395] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:53,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:53,395] [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
Maribellus luteus	strain=XSD2	GCA_003576475.1	2305463	2305463	type	True	100.0	1960	1962	95	conclusive
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	78.1699	492	1962	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	77.7581	418	1962	95	below_threshold
Draconibacterium mangrovi	strain=GM2-18	GCA_010586825.1	2697469	2697469	type	True	77.7505	430	1962	95	below_threshold
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	77.7412	426	1962	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	77.6645	419	1962	95	below_threshold
Draconibacterium halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	77.3221	339	1962	95	below_threshold
Mariniphaga anaerophila	strain=DSM 26910	GCA_900129025.1	1484053	1484053	type	True	76.8821	205	1962	95	below_threshold
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	76.6853	216	1962	95	below_threshold
Mangrovibacterium diazotrophicum	strain=DSM 27148	GCA_003610535.1	1261403	1261403	type	True	76.6295	105	1962	95	below_threshold
Tangfeifania diversioriginum	strain=DSM 27063	GCA_900141875.1	1168035	1168035	type	True	76.3385	198	1962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,397] [INFO] DFAST Taxonomy check result was written to GCF_003576475.1_ASM357647v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:53,398] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:53,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:53,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference/checkm_data
[2024-01-24 11:27:53,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:53,460] [INFO] Task started: CheckM
[2024-01-24 11:27:53,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003576475.1_ASM357647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003576475.1_ASM357647v1_genomic.fna/checkm_input GCF_003576475.1_ASM357647v1_genomic.fna/checkm_result
[2024-01-24 11:29:14,658] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:14,659] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.88%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:14,682] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:14,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:14,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003576475.1_ASM357647v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:14,683] [INFO] Task started: Blastn
[2024-01-24 11:29:14,684] [INFO] Running command: blastn -query GCF_003576475.1_ASM357647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6121c3e-813d-435d-9c51-ca91db45b118/dqc_reference/reference_markers_gtdb.fasta -out GCF_003576475.1_ASM357647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:15,549] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:15,554] [INFO] Selected 17 target genomes.
[2024-01-24 11:29:15,554] [INFO] Target genome list was writen to GCF_003576475.1_ASM357647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:15,576] [INFO] Task started: fastANI
[2024-01-24 11:29:15,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg9868d03e-ede7-41cc-ad75-fb0e4d79dcd7/GCF_003576475.1_ASM357647v1_genomic.fna.gz --refList GCF_003576475.1_ASM357647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003576475.1_ASM357647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:29,817] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:29,833] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:29,833] [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_003576475.1	s__Draconibacterium luteum	100.0	1960	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011799805.1	s__Draconibacterium sp011799805	78.1704	492	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCA_011620585.1	s__Draconibacterium sp011620585	77.9042	373	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626635.1	s__Draconibacterium orientale	77.7632	416	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010586825.1	s__Draconibacterium mangrovi	77.7505	430	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949475.1	s__Draconibacterium sediminis	77.7415	426	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010448835.1	s__Draconibacterium halophilum	77.3288	336	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129025.1	s__Mariniphaga anaerophila	76.8482	208	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610535.1	s__Mangrovibacterium diazotrophicum	76.6509	105	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141875.1	s__Tangfeifania diversioriginum	76.3385	198	1962	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Tangfeifania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:29:29,835] [INFO] GTDB search result was written to GCF_003576475.1_ASM357647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:29,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:29,838] [INFO] DFAST_QC result json was written to GCF_003576475.1_ASM357647v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:29,838] [INFO] DFAST_QC completed!
[2024-01-24 11:29:29,838] [INFO] Total running time: 0h2m25s