[2024-01-25 19:35:51,369] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:51,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:51,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference
[2024-01-25 19:35:52,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:52,639] [INFO] Task started: Prodigal
[2024-01-25 19:35:52,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f92d80f-b7d8-48e9-ba21-c1046f1000a0/GCF_002954325.1_ASM295432v1_genomic.fna.gz | prodigal -d GCF_002954325.1_ASM295432v1_genomic.fna/cds.fna -a GCF_002954325.1_ASM295432v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:05,425] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:05,425] [INFO] Task started: HMMsearch
[2024-01-25 19:36:05,425] [INFO] Running command: hmmsearch --tblout GCF_002954325.1_ASM295432v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference/reference_markers.hmm GCF_002954325.1_ASM295432v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:05,649] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:05,650] [INFO] Found 6/6 markers.
[2024-01-25 19:36:05,677] [INFO] Query marker FASTA was written to GCF_002954325.1_ASM295432v1_genomic.fna/markers.fasta
[2024-01-25 19:36:05,677] [INFO] Task started: Blastn
[2024-01-25 19:36:05,677] [INFO] Running command: blastn -query GCF_002954325.1_ASM295432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference/reference_markers.fasta -out GCF_002954325.1_ASM295432v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:06,266] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:06,271] [INFO] Selected 30 target genomes.
[2024-01-25 19:36:06,272] [INFO] Target genome list was writen to GCF_002954325.1_ASM295432v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:06,290] [INFO] Task started: fastANI
[2024-01-25 19:36:06,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f92d80f-b7d8-48e9-ba21-c1046f1000a0/GCF_002954325.1_ASM295432v1_genomic.fna.gz --refList GCF_002954325.1_ASM295432v1_genomic.fna/target_genomes.txt --output GCF_002954325.1_ASM295432v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:24,384] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:24,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:24,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:24,395] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:24,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:24,395] [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
Aureicoccus marinus	strain=SG-18	GCA_002954325.1	754435	754435	type	True	99.9998	1014	1016	95	conclusive
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	76.9714	61	1016	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	76.8549	63	1016	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	76.7843	55	1016	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.7501	62	1016	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.6543	76	1016	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.6543	76	1016	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.6104	79	1016	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.5829	80	1016	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	76.5296	74	1016	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	76.5225	79	1016	95	below_threshold
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	76.4156	68	1016	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.3745	75	1016	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.3406	51	1016	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	76.3242	65	1016	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.2464	56	1016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:24,396] [INFO] DFAST Taxonomy check result was written to GCF_002954325.1_ASM295432v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:24,398] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:24,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:24,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference/checkm_data
[2024-01-25 19:36:24,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:24,432] [INFO] Task started: CheckM
[2024-01-25 19:36:24,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002954325.1_ASM295432v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002954325.1_ASM295432v1_genomic.fna/checkm_input GCF_002954325.1_ASM295432v1_genomic.fna/checkm_result
[2024-01-25 19:37:02,378] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:02,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:02,398] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:02,399] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:02,399] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002954325.1_ASM295432v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:02,399] [INFO] Task started: Blastn
[2024-01-25 19:37:02,399] [INFO] Running command: blastn -query GCF_002954325.1_ASM295432v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fbea24b-ff47-4e08-a4d2-e7c98023ff3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002954325.1_ASM295432v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:03,215] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:03,224] [INFO] Selected 28 target genomes.
[2024-01-25 19:37:03,224] [INFO] Target genome list was writen to GCF_002954325.1_ASM295432v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:03,237] [INFO] Task started: fastANI
[2024-01-25 19:37:03,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f92d80f-b7d8-48e9-ba21-c1046f1000a0/GCF_002954325.1_ASM295432v1_genomic.fna.gz --refList GCF_002954325.1_ASM295432v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002954325.1_ASM295432v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:20,588] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:20,599] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:20,599] [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_002954325.1	s__Aureicoccus marinus	99.9998	1014	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003058265.1	s__Muricauda sp003058265	77.0145	60	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	77.0024	68	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.8632	71	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_003057865.1	s__Muricauda brasiliensis	76.7843	55	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_003584165.1	s__Muricauda sp003584165	76.7088	74	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.5812	79	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005937185.1	s__Muricauda algicola	76.5722	77	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	76.5296	74	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCA_013911645.1	s__Muricauda sp013911645	76.5263	74	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001695.1	s__Muricauda pacifica	76.4459	67	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	76.4354	59	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	76.4265	73	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_017313785.1	s__Muricauda sp002711825	76.3829	63	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.3331	50	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_001683915.1	s__Muricauda sp001683915	76.3139	75	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCA_002699205.1	s__Muricauda sp002699205	76.1831	73	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:20,600] [INFO] GTDB search result was written to GCF_002954325.1_ASM295432v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:20,601] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:20,604] [INFO] DFAST_QC result json was written to GCF_002954325.1_ASM295432v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:20,605] [INFO] DFAST_QC completed!
[2024-01-25 19:37:20,605] [INFO] Total running time: 0h1m29s