[2024-01-24 13:25:29,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference
[2024-01-24 13:25:31,205] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:31,205] [INFO] Task started: Prodigal
[2024-01-24 13:25:31,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5685c04-465a-4baf-9270-bfb228f53776/GCF_900078205.2_PRJEB13113_genomic.fna.gz | prodigal -d GCF_900078205.2_PRJEB13113_genomic.fna/cds.fna -a GCF_900078205.2_PRJEB13113_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:51,592] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:51,593] [INFO] Task started: HMMsearch
[2024-01-24 13:25:51,593] [INFO] Running command: hmmsearch --tblout GCF_900078205.2_PRJEB13113_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference/reference_markers.hmm GCF_900078205.2_PRJEB13113_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:51,898] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:51,900] [INFO] Found 6/6 markers.
[2024-01-24 13:25:51,943] [INFO] Query marker FASTA was written to GCF_900078205.2_PRJEB13113_genomic.fna/markers.fasta
[2024-01-24 13:25:51,944] [INFO] Task started: Blastn
[2024-01-24 13:25:51,944] [INFO] Running command: blastn -query GCF_900078205.2_PRJEB13113_genomic.fna/markers.fasta -db /var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference/reference_markers.fasta -out GCF_900078205.2_PRJEB13113_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:52,606] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:52,610] [INFO] Selected 13 target genomes.
[2024-01-24 13:25:52,610] [INFO] Target genome list was writen to GCF_900078205.2_PRJEB13113_genomic.fna/target_genomes.txt
[2024-01-24 13:25:52,616] [INFO] Task started: fastANI
[2024-01-24 13:25:52,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5685c04-465a-4baf-9270-bfb228f53776/GCF_900078205.2_PRJEB13113_genomic.fna.gz --refList GCF_900078205.2_PRJEB13113_genomic.fna/target_genomes.txt --output GCF_900078205.2_PRJEB13113_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:06,142] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:06,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:06,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:06,159] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:26:06,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:26:06,159] [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
Chryseobacterium nakagawai	strain=NCTC13529	GCA_900637665.1	1241982	1241982	type	True	87.6924	1403	1792	95	below_threshold
Chryseobacterium jejuense	strain=DSM 19299	GCA_900100075.1	445960	445960	type	True	87.4957	1414	1792	95	below_threshold
Chryseobacterium contaminans	strain=C-26	GCA_001684955.1	1423959	1423959	type	True	87.3934	1164	1792	95	below_threshold
Chryseobacterium contaminans	strain=DSM 27621	GCA_900142615.1	1423959	1423959	type	True	87.2697	1300	1792	95	below_threshold
Chryseobacterium pennae	strain=1_F178	GCA_003385515.1	2258962	2258962	type	True	86.9221	1365	1792	95	below_threshold
Chryseobacterium ureilyticum	strain=DSM 18017	GCA_900156735.1	373668	373668	type	True	84.5452	1203	1792	95	below_threshold
Chryseobacterium artocarpi	strain=UTM-3	GCA_001684975.1	1414727	1414727	type	True	84.3173	1190	1792	95	below_threshold
Chryseobacterium arthrosphaerae	strain=CC-VM-7	GCA_001684965.1	651561	651561	type	True	83.0361	1117	1792	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.5766	695	1792	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.0259	737	1792	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.4181	588	1792	95	below_threshold
Kaistella carnis	strain=G0081	GCA_003860585.1	1241979	1241979	type	True	77.1322	157	1792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:06,161] [INFO] DFAST Taxonomy check result was written to GCF_900078205.2_PRJEB13113_genomic.fna/tc_result.tsv
[2024-01-24 13:26:06,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:06,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:06,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference/checkm_data
[2024-01-24 13:26:06,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:06,220] [INFO] Task started: CheckM
[2024-01-24 13:26:06,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900078205.2_PRJEB13113_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900078205.2_PRJEB13113_genomic.fna/checkm_input GCF_900078205.2_PRJEB13113_genomic.fna/checkm_result
[2024-01-24 13:27:04,162] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:04,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:04,190] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:04,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:04,191] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900078205.2_PRJEB13113_genomic.fna/markers.fasta)
[2024-01-24 13:27:04,191] [INFO] Task started: Blastn
[2024-01-24 13:27:04,192] [INFO] Running command: blastn -query GCF_900078205.2_PRJEB13113_genomic.fna/markers.fasta -db /var/lib/cwl/stg538149b6-dc48-4f74-a480-8f3d27e378d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900078205.2_PRJEB13113_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:05,130] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:05,134] [INFO] Selected 14 target genomes.
[2024-01-24 13:27:05,134] [INFO] Target genome list was writen to GCF_900078205.2_PRJEB13113_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:05,150] [INFO] Task started: fastANI
[2024-01-24 13:27:05,150] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5685c04-465a-4baf-9270-bfb228f53776/GCF_900078205.2_PRJEB13113_genomic.fna.gz --refList GCF_900078205.2_PRJEB13113_genomic.fna/target_genomes_gtdb.txt --output GCF_900078205.2_PRJEB13113_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:22,847] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:22,862] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:22,863] [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_900078205.2	s__Chryseobacterium timonianum	100.0	1792	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003815715.1	s__Chryseobacterium sp003815715	87.8155	1401	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637665.1	s__Chryseobacterium nakagawai	87.6924	1403	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100075.1	s__Chryseobacterium jejuense	87.4867	1415	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_004119455.1	s__Chryseobacterium sp004119455	87.4296	1338	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017877355.1	s__Chryseobacterium jejuense_A	87.4146	1387	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684955.1	s__Chryseobacterium contaminans	87.4045	1163	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000829375.1	s__Chryseobacterium sp000829375	87.2485	1395	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218825.1	s__Chryseobacterium bernardetii	87.1862	1354	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.97	99.97	0.99	0.99	3	-
GCF_009900745.1	s__Chryseobacterium sp009900745	86.585	1361	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003815975.1	s__Chryseobacterium bernardetii_A	86.3813	1283	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.90	0.90	2	-
GCF_001684975.1	s__Chryseobacterium artocarpi	84.3035	1192	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835665.1	s__Chryseobacterium sp002835665	83.4082	896	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236175.1	s__Chryseobacterium sp019236175	82.6259	1043	1792	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:22,864] [INFO] GTDB search result was written to GCF_900078205.2_PRJEB13113_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:22,865] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:22,869] [INFO] DFAST_QC result json was written to GCF_900078205.2_PRJEB13113_genomic.fna/dqc_result.json
[2024-01-24 13:27:22,869] [INFO] DFAST_QC completed!
[2024-01-24 13:27:22,869] [INFO] Total running time: 0h1m53s