[2024-01-24 14:46:49,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:49,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:49,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference
[2024-01-24 14:46:53,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:53,978] [INFO] Task started: Prodigal
[2024-01-24 14:46:53,978] [INFO] Running command: gunzip -c /var/lib/cwl/stgb137cf42-ebfb-4523-acee-b899b99f87bc/GCF_005937185.1_ASM593718v1_genomic.fna.gz | prodigal -d GCF_005937185.1_ASM593718v1_genomic.fna/cds.fna -a GCF_005937185.1_ASM593718v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:19,495] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:19,495] [INFO] Task started: HMMsearch
[2024-01-24 14:47:19,496] [INFO] Running command: hmmsearch --tblout GCF_005937185.1_ASM593718v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference/reference_markers.hmm GCF_005937185.1_ASM593718v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:19,851] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:19,853] [INFO] Found 6/6 markers.
[2024-01-24 14:47:19,924] [INFO] Query marker FASTA was written to GCF_005937185.1_ASM593718v1_genomic.fna/markers.fasta
[2024-01-24 14:47:19,925] [INFO] Task started: Blastn
[2024-01-24 14:47:19,925] [INFO] Running command: blastn -query GCF_005937185.1_ASM593718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference/reference_markers.fasta -out GCF_005937185.1_ASM593718v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:20,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:20,667] [INFO] Selected 19 target genomes.
[2024-01-24 14:47:20,667] [INFO] Target genome list was writen to GCF_005937185.1_ASM593718v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:20,675] [INFO] Task started: fastANI
[2024-01-24 14:47:20,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgb137cf42-ebfb-4523-acee-b899b99f87bc/GCF_005937185.1_ASM593718v1_genomic.fna.gz --refList GCF_005937185.1_ASM593718v1_genomic.fna/target_genomes.txt --output GCF_005937185.1_ASM593718v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:35,196] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:35,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:35,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:35,213] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:35,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:35,213] [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 algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	100.0	1509	1509	95	conclusive
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	79.1165	529	1509	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	78.3615	448	1509	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	78.3508	370	1509	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	78.1038	343	1509	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	78.0354	324	1509	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	77.9972	332	1509	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.8695	343	1509	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	77.8141	251	1509	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	77.7831	277	1509	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	77.7681	252	1509	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	77.7615	228	1509	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	77.7144	254	1509	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	77.6294	248	1509	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.6279	278	1509	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.566	273	1509	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.5341	283	1509	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	77.468	269	1509	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.4174	264	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:35,215] [INFO] DFAST Taxonomy check result was written to GCF_005937185.1_ASM593718v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:35,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:35,215] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:35,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference/checkm_data
[2024-01-24 14:47:35,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:35,262] [INFO] Task started: CheckM
[2024-01-24 14:47:35,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005937185.1_ASM593718v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005937185.1_ASM593718v1_genomic.fna/checkm_input GCF_005937185.1_ASM593718v1_genomic.fna/checkm_result
[2024-01-24 14:48:47,761] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:47,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:47,782] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:47,782] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:47,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005937185.1_ASM593718v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:47,783] [INFO] Task started: Blastn
[2024-01-24 14:48:47,783] [INFO] Running command: blastn -query GCF_005937185.1_ASM593718v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7905a1-3d72-485d-bebd-384369ccf11e/dqc_reference/reference_markers_gtdb.fasta -out GCF_005937185.1_ASM593718v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:48,746] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:48,750] [INFO] Selected 19 target genomes.
[2024-01-24 14:48:48,750] [INFO] Target genome list was writen to GCF_005937185.1_ASM593718v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:48,767] [INFO] Task started: fastANI
[2024-01-24 14:48:48,767] [INFO] Running command: fastANI --query /var/lib/cwl/stgb137cf42-ebfb-4523-acee-b899b99f87bc/GCF_005937185.1_ASM593718v1_genomic.fna.gz --refList GCF_005937185.1_ASM593718v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005937185.1_ASM593718v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:04,491] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:04,511] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:04,511] [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_005937185.1	s__Muricauda algicola	100.0	1509	1509	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_900129665.1	s__Muricauda flava	79.1212	529	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	78.5188	377	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	78.3809	407	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	78.3697	447	1509	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	78.3438	370	1509	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	78.0477	331	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_017313225.1	s__Muricauda sp017313225	78.0186	334	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	78.0134	351	1509	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	77.9224	333	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	77.8787	342	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745185.1	s__Muricauda sp000745185	77.8146	341	1509	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	77.8128	277	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	77.8104	252	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	77.7799	278	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	77.7615	228	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_003385855.1	s__Muricauda sp003385855	77.7577	345	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	77.6253	279	1509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013911645.1	s__Muricauda sp013911645	77.5302	267	1509	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 14:49:04,513] [INFO] GTDB search result was written to GCF_005937185.1_ASM593718v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:04,514] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:04,519] [INFO] DFAST_QC result json was written to GCF_005937185.1_ASM593718v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:04,519] [INFO] DFAST_QC completed!
[2024-01-24 14:49:04,519] [INFO] Total running time: 0h2m15s