[2024-01-24 15:18:19,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,550] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference
[2024-01-24 15:18:25,005] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:25,007] [INFO] Task started: Prodigal
[2024-01-24 15:18:25,008] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cb856ec-e30e-4c58-b319-01392dd14c4c/GCF_019880545.1_ASM1988054v1_genomic.fna.gz | prodigal -d GCF_019880545.1_ASM1988054v1_genomic.fna/cds.fna -a GCF_019880545.1_ASM1988054v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:45,354] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:45,354] [INFO] Task started: HMMsearch
[2024-01-24 15:18:45,355] [INFO] Running command: hmmsearch --tblout GCF_019880545.1_ASM1988054v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference/reference_markers.hmm GCF_019880545.1_ASM1988054v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:45,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:45,634] [INFO] Found 6/6 markers.
[2024-01-24 15:18:45,670] [INFO] Query marker FASTA was written to GCF_019880545.1_ASM1988054v1_genomic.fna/markers.fasta
[2024-01-24 15:18:45,670] [INFO] Task started: Blastn
[2024-01-24 15:18:45,670] [INFO] Running command: blastn -query GCF_019880545.1_ASM1988054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference/reference_markers.fasta -out GCF_019880545.1_ASM1988054v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:46,310] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:46,315] [INFO] Selected 21 target genomes.
[2024-01-24 15:18:46,316] [INFO] Target genome list was writen to GCF_019880545.1_ASM1988054v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:46,326] [INFO] Task started: fastANI
[2024-01-24 15:18:46,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cb856ec-e30e-4c58-b319-01392dd14c4c/GCF_019880545.1_ASM1988054v1_genomic.fna.gz --refList GCF_019880545.1_ASM1988054v1_genomic.fna/target_genomes.txt --output GCF_019880545.1_ASM1988054v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:01,090] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:01,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:01,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:01,112] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:01,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:01,112] [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 ochracea	strain=JGD-17	GCA_009903685.1	2696472	2696472	type	True	80.212	609	1063	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	77.9877	342	1063	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	77.9524	341	1063	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	77.9124	351	1063	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	77.8677	323	1063	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.7969	301	1063	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.7876	347	1063	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	77.7835	322	1063	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	77.6615	336	1063	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.6481	254	1063	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.5709	278	1063	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.4505	248	1063	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.3781	205	1063	95	below_threshold
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	77.0441	195	1063	95	below_threshold
Maribacter aurantiacus	strain=KCTC 52409	GCA_005780245.1	1882343	1882343	type	True	76.3443	125	1063	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	76.3147	68	1063	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:01,115] [INFO] DFAST Taxonomy check result was written to GCF_019880545.1_ASM1988054v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:01,115] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:01,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:01,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference/checkm_data
[2024-01-24 15:19:01,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:01,156] [INFO] Task started: CheckM
[2024-01-24 15:19:01,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019880545.1_ASM1988054v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019880545.1_ASM1988054v1_genomic.fna/checkm_input GCF_019880545.1_ASM1988054v1_genomic.fna/checkm_result
[2024-01-24 15:19:58,461] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:58,462] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:58,484] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:58,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:58,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019880545.1_ASM1988054v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:58,485] [INFO] Task started: Blastn
[2024-01-24 15:19:58,485] [INFO] Running command: blastn -query GCF_019880545.1_ASM1988054v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg088a5002-d958-4e1d-87f7-74aa95bab467/dqc_reference/reference_markers_gtdb.fasta -out GCF_019880545.1_ASM1988054v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:59,304] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:59,311] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:59,311] [INFO] Target genome list was writen to GCF_019880545.1_ASM1988054v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:59,323] [INFO] Task started: fastANI
[2024-01-24 15:19:59,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cb856ec-e30e-4c58-b319-01392dd14c4c/GCF_019880545.1_ASM1988054v1_genomic.fna.gz --refList GCF_019880545.1_ASM1988054v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019880545.1_ASM1988054v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:12,865] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:12,880] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:20:12,880] [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_009903685.1	s__Muricauda ochracea	80.2214	608	1063	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	78.2379	376	1063	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	78.1793	345	1063	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	78.086	361	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_004916895.1	s__Muricauda alvinocaridis	77.998	341	1063	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	77.9912	353	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058265.1	s__Muricauda sp003058265	77.9627	340	1063	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	77.9033	352	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_007785775.2	s__Muricauda sp003973595	77.8677	323	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_013090115.1	s__Muricauda amphidinii	77.7969	301	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	77.7915	332	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584105.1	s__Muricauda taeanensis	77.6712	335	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_000224085.1	s__Muricauda ruestringensis	77.6481	254	1063	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	77.5873	268	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795065.1	s__Muricauda sp017795065	77.578	248	1063	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	77.4131	243	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	77.3925	204	1063	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	77.0117	211	1063	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 15:20:12,882] [INFO] GTDB search result was written to GCF_019880545.1_ASM1988054v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:12,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:12,886] [INFO] DFAST_QC result json was written to GCF_019880545.1_ASM1988054v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:12,886] [INFO] DFAST_QC completed!
[2024-01-24 15:20:12,886] [INFO] Total running time: 0h1m53s