[2024-01-25 20:03:20,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:20,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:20,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference
[2024-01-25 20:03:21,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:21,679] [INFO] Task started: Prodigal
[2024-01-25 20:03:21,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg886d599f-a52a-4014-838b-061b58aba26d/GCF_017355955.1_ASM1735595v1_genomic.fna.gz | prodigal -d GCF_017355955.1_ASM1735595v1_genomic.fna/cds.fna -a GCF_017355955.1_ASM1735595v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:49,410] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:49,411] [INFO] Task started: HMMsearch
[2024-01-25 20:03:49,411] [INFO] Running command: hmmsearch --tblout GCF_017355955.1_ASM1735595v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference/reference_markers.hmm GCF_017355955.1_ASM1735595v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:49,778] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:49,781] [INFO] Found 6/6 markers.
[2024-01-25 20:03:49,832] [INFO] Query marker FASTA was written to GCF_017355955.1_ASM1735595v1_genomic.fna/markers.fasta
[2024-01-25 20:03:49,832] [INFO] Task started: Blastn
[2024-01-25 20:03:49,832] [INFO] Running command: blastn -query GCF_017355955.1_ASM1735595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference/reference_markers.fasta -out GCF_017355955.1_ASM1735595v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:50,420] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:50,422] [INFO] Selected 11 target genomes.
[2024-01-25 20:03:50,423] [INFO] Target genome list was writen to GCF_017355955.1_ASM1735595v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:50,434] [INFO] Task started: fastANI
[2024-01-25 20:03:50,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg886d599f-a52a-4014-838b-061b58aba26d/GCF_017355955.1_ASM1735595v1_genomic.fna.gz --refList GCF_017355955.1_ASM1735595v1_genomic.fna/target_genomes.txt --output GCF_017355955.1_ASM1735595v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:01,929] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:01,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:01,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:01,938] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:04:01,938] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:04:01,938] [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
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	82.0116	1188	2027	95	below_threshold
Rufibacter sediminis	strain=H-1	GCA_014269285.1	2762756	2762756	type	True	81.7696	1088	2027	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	81.677	1117	2027	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	81.4585	1127	2027	95	below_threshold
Rufibacter immobilis	strain=MCC P1	GCA_003721565.1	1348778	1348778	type	True	81.1344	973	2027	95	below_threshold
Rufibacter glacialis	strain=CGMCC 1.9789	GCA_014645715.1	1259555	1259555	type	True	80.5561	944	2027	95	below_threshold
Rufibacter tibetensis	strain=1351	GCA_001310085.1	512763	512763	type	True	80.4883	880	2027	95	below_threshold
Rufibacter glacialis	strain=MDT1-10-3	GCA_008271745.1	1259555	1259555	type	True	80.4661	956	2027	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	76.8498	188	2027	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	76.5924	108	2027	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	76.5797	220	2027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:01,941] [INFO] DFAST Taxonomy check result was written to GCF_017355955.1_ASM1735595v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:01,942] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:01,942] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:01,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference/checkm_data
[2024-01-25 20:04:01,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:02,002] [INFO] Task started: CheckM
[2024-01-25 20:04:02,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017355955.1_ASM1735595v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017355955.1_ASM1735595v1_genomic.fna/checkm_input GCF_017355955.1_ASM1735595v1_genomic.fna/checkm_result
[2024-01-25 20:05:14,655] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:14,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:14,682] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:14,682] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:14,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017355955.1_ASM1735595v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:14,683] [INFO] Task started: Blastn
[2024-01-25 20:05:14,683] [INFO] Running command: blastn -query GCF_017355955.1_ASM1735595v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86f6fd7e-1151-42fe-8048-56314f18f6e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_017355955.1_ASM1735595v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:15,549] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:15,553] [INFO] Selected 8 target genomes.
[2024-01-25 20:05:15,553] [INFO] Target genome list was writen to GCF_017355955.1_ASM1735595v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:15,564] [INFO] Task started: fastANI
[2024-01-25 20:05:15,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg886d599f-a52a-4014-838b-061b58aba26d/GCF_017355955.1_ASM1735595v1_genomic.fna.gz --refList GCF_017355955.1_ASM1735595v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017355955.1_ASM1735595v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:26,696] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:26,702] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:26,702] [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_017355955.1	s__Rufibacter sp017355955	100.0	2027	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016924645.1	s__Rufibacter sp016924645	85.6116	1270	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916365.1	s__Rufibacter sp017916365	82.5285	1189	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	95.42	95.42	0.94	0.94	2	-
GCF_008271695.1	s__Rufibacter sp008271695	82.0162	1187	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014269285.1	s__Rufibacter sediminis	81.7562	1090	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721565.1	s__Rufibacter immobilis	81.1231	975	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623775.1	s__Rufibacter sp013623775	80.8045	965	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310085.1	s__Rufibacter tibetensis	80.4948	879	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:26,704] [INFO] GTDB search result was written to GCF_017355955.1_ASM1735595v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:26,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:26,707] [INFO] DFAST_QC result json was written to GCF_017355955.1_ASM1735595v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:26,707] [INFO] DFAST_QC completed!
[2024-01-25 20:05:26,707] [INFO] Total running time: 0h2m6s