[2024-01-25 20:23:50,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:50,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:50,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference
[2024-01-25 20:23:51,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:51,637] [INFO] Task started: Prodigal
[2024-01-25 20:23:51,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg27efd581-8934-47f0-ac88-fd07a0dadb00/GCF_012931685.1_ASM1293168v1_genomic.fna.gz | prodigal -d GCF_012931685.1_ASM1293168v1_genomic.fna/cds.fna -a GCF_012931685.1_ASM1293168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:00,802] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:00,802] [INFO] Task started: HMMsearch
[2024-01-25 20:24:00,802] [INFO] Running command: hmmsearch --tblout GCF_012931685.1_ASM1293168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference/reference_markers.hmm GCF_012931685.1_ASM1293168v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:01,045] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:01,048] [INFO] Found 6/6 markers.
[2024-01-25 20:24:01,083] [INFO] Query marker FASTA was written to GCF_012931685.1_ASM1293168v1_genomic.fna/markers.fasta
[2024-01-25 20:24:01,083] [INFO] Task started: Blastn
[2024-01-25 20:24:01,083] [INFO] Running command: blastn -query GCF_012931685.1_ASM1293168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference/reference_markers.fasta -out GCF_012931685.1_ASM1293168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:01,745] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:01,748] [INFO] Selected 14 target genomes.
[2024-01-25 20:24:01,748] [INFO] Target genome list was writen to GCF_012931685.1_ASM1293168v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:01,759] [INFO] Task started: fastANI
[2024-01-25 20:24:01,759] [INFO] Running command: fastANI --query /var/lib/cwl/stg27efd581-8934-47f0-ac88-fd07a0dadb00/GCF_012931685.1_ASM1293168v1_genomic.fna.gz --refList GCF_012931685.1_ASM1293168v1_genomic.fna/target_genomes.txt --output GCF_012931685.1_ASM1293168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:11,546] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:11,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:11,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:11,556] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:24:11,556] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:11,556] [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
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	100.0	1051	1052	95	conclusive
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	80.5843	580	1052	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	80.2877	598	1052	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	79.9918	608	1052	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	78.5971	376	1052	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	78.2853	395	1052	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.9814	247	1052	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.8347	239	1052	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.7737	195	1052	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.6964	194	1052	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.6612	230	1052	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.581	249	1052	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.3194	303	1052	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	77.0625	174	1052	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:11,557] [INFO] DFAST Taxonomy check result was written to GCF_012931685.1_ASM1293168v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:11,558] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:11,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:11,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference/checkm_data
[2024-01-25 20:24:11,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:11,593] [INFO] Task started: CheckM
[2024-01-25 20:24:11,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012931685.1_ASM1293168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012931685.1_ASM1293168v1_genomic.fna/checkm_input GCF_012931685.1_ASM1293168v1_genomic.fna/checkm_result
[2024-01-25 20:24:42,048] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:42,049] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:42,067] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:42,067] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:42,068] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012931685.1_ASM1293168v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:42,068] [INFO] Task started: Blastn
[2024-01-25 20:24:42,068] [INFO] Running command: blastn -query GCF_012931685.1_ASM1293168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg199890b7-6352-4549-8e37-1d94300e9c09/dqc_reference/reference_markers_gtdb.fasta -out GCF_012931685.1_ASM1293168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:43,027] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:43,030] [INFO] Selected 18 target genomes.
[2024-01-25 20:24:43,030] [INFO] Target genome list was writen to GCF_012931685.1_ASM1293168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:43,095] [INFO] Task started: fastANI
[2024-01-25 20:24:43,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg27efd581-8934-47f0-ac88-fd07a0dadb00/GCF_012931685.1_ASM1293168v1_genomic.fna.gz --refList GCF_012931685.1_ASM1293168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012931685.1_ASM1293168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:54,085] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:54,096] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:54,096] [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_012931685.1	s__Pseudobizionia ponticola	100.0	1051	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	conclusive
GCF_002895005.1	s__Hanstruepera neustonica	79.9867	609	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hanstruepera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115185.1	s__Algorimicrobium echini	78.6009	375	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCF_003148645.1	s__Xanthomarina spongicola	78.3768	376	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086165.1	s__Algorimicrobium algoritergicola	78.2871	393	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008086205.1	s__Algorimicrobium myxarmorum	78.2575	318	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	78.0951	299	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	78.0464	278	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.9963	297	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.98	283	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.8347	239	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	77.7094	194	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.6706	227	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	77.581	249	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403915.1	s__Winogradskyella pacifica	77.3698	212	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	97.90	97.90	0.94	0.94	2	-
GCF_001418105.1	s__Oceanihabitans himadriensis	77.3243	301	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129745.1	s__Winogradskyella jejuensis	77.0625	174	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042715.1	s__Site-B15 sp013042715	76.9395	142	1052	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Site-B15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:54,098] [INFO] GTDB search result was written to GCF_012931685.1_ASM1293168v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:54,098] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:54,101] [INFO] DFAST_QC result json was written to GCF_012931685.1_ASM1293168v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:54,101] [INFO] DFAST_QC completed!
[2024-01-25 20:24:54,102] [INFO] Total running time: 0h1m4s