[2024-01-24 13:55:15,190] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:15,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:15,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference
[2024-01-24 13:55:16,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:16,575] [INFO] Task started: Prodigal
[2024-01-24 13:55:16,576] [INFO] Running command: gunzip -c /var/lib/cwl/stgd571cc8f-c6be-482c-b815-0a3d5cef9b74/GCF_013090115.1_ASM1309011v1_genomic.fna.gz | prodigal -d GCF_013090115.1_ASM1309011v1_genomic.fna/cds.fna -a GCF_013090115.1_ASM1309011v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:36,290] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:36,291] [INFO] Task started: HMMsearch
[2024-01-24 13:55:36,291] [INFO] Running command: hmmsearch --tblout GCF_013090115.1_ASM1309011v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference/reference_markers.hmm GCF_013090115.1_ASM1309011v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:36,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:36,554] [INFO] Found 6/6 markers.
[2024-01-24 13:55:36,588] [INFO] Query marker FASTA was written to GCF_013090115.1_ASM1309011v1_genomic.fna/markers.fasta
[2024-01-24 13:55:36,589] [INFO] Task started: Blastn
[2024-01-24 13:55:36,589] [INFO] Running command: blastn -query GCF_013090115.1_ASM1309011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference/reference_markers.fasta -out GCF_013090115.1_ASM1309011v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:37,248] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:37,252] [INFO] Selected 17 target genomes.
[2024-01-24 13:55:37,252] [INFO] Target genome list was writen to GCF_013090115.1_ASM1309011v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:37,272] [INFO] Task started: fastANI
[2024-01-24 13:55:37,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgd571cc8f-c6be-482c-b815-0a3d5cef9b74/GCF_013090115.1_ASM1309011v1_genomic.fna.gz --refList GCF_013090115.1_ASM1309011v1_genomic.fna/target_genomes.txt --output GCF_013090115.1_ASM1309011v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:50,187] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:50,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:50,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:50,201] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:50,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:50,201] [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
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	100.0	1267	1270	95	conclusive
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	79.3798	568	1270	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	78.1546	384	1270	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	78.0729	401	1270	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	77.9693	374	1270	95	below_threshold
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	77.9674	343	1270	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	77.9497	344	1270	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	77.845	345	1270	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.774	341	1270	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.7601	352	1270	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	77.6801	306	1270	95	below_threshold
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	77.6263	254	1270	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.5875	292	1270	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.1552	292	1270	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.3709	102	1270	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.9758	53	1270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:50,203] [INFO] DFAST Taxonomy check result was written to GCF_013090115.1_ASM1309011v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:50,203] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:50,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:50,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference/checkm_data
[2024-01-24 13:55:50,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:50,245] [INFO] Task started: CheckM
[2024-01-24 13:55:50,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013090115.1_ASM1309011v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013090115.1_ASM1309011v1_genomic.fna/checkm_input GCF_013090115.1_ASM1309011v1_genomic.fna/checkm_result
[2024-01-24 13:56:47,409] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:47,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:47,430] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:47,431] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:47,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013090115.1_ASM1309011v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:47,432] [INFO] Task started: Blastn
[2024-01-24 13:56:47,432] [INFO] Running command: blastn -query GCF_013090115.1_ASM1309011v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e9fea55-f712-461f-bf4f-9f51fbaed731/dqc_reference/reference_markers_gtdb.fasta -out GCF_013090115.1_ASM1309011v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:48,303] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:48,308] [INFO] Selected 18 target genomes.
[2024-01-24 13:56:48,308] [INFO] Target genome list was writen to GCF_013090115.1_ASM1309011v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:48,329] [INFO] Task started: fastANI
[2024-01-24 13:56:48,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgd571cc8f-c6be-482c-b815-0a3d5cef9b74/GCF_013090115.1_ASM1309011v1_genomic.fna.gz --refList GCF_013090115.1_ASM1309011v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013090115.1_ASM1309011v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:01,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:01,482] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:01,483] [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_013090115.1	s__Muricauda amphidinii	100.0	1267	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003382275.1	s__Muricauda nanhaiensis	79.3971	566	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	78.1922	392	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_000745185.1	s__Muricauda sp000745185	78.1652	412	1270	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	78.1546	384	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_003385855.1	s__Muricauda sp003385855	78.1409	388	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_900215465.1	s__Muricauda pacifica_A	78.077	400	1270	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	78.0673	410	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	78.0473	379	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	77.9783	373	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005937185.1	s__Muricauda algicola	77.9674	343	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	77.9598	343	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413955.1	s__Muricauda eckloniae	77.9244	364	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	77.8439	345	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	77.8378	303	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	77.783	340	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010993815.1	s__Muricauda sp010993815	77.5768	320	1270	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	77.5	313	1270	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:01,484] [INFO] GTDB search result was written to GCF_013090115.1_ASM1309011v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:01,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:01,489] [INFO] DFAST_QC result json was written to GCF_013090115.1_ASM1309011v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:01,489] [INFO] DFAST_QC completed!
[2024-01-24 13:57:01,489] [INFO] Total running time: 0h1m46s