[2024-01-24 14:05:36,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,047] [INFO] DQC Reference Directory: /var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference
[2024-01-24 14:05:37,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:37,398] [INFO] Task started: Prodigal
[2024-01-24 14:05:37,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e9c611a-1120-4920-9272-1722234f7b77/GCF_000830985.1_ASM83098v1_genomic.fna.gz | prodigal -d GCF_000830985.1_ASM83098v1_genomic.fna/cds.fna -a GCF_000830985.1_ASM83098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:50,235] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:50,236] [INFO] Task started: HMMsearch
[2024-01-24 14:05:50,236] [INFO] Running command: hmmsearch --tblout GCF_000830985.1_ASM83098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference/reference_markers.hmm GCF_000830985.1_ASM83098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:50,581] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:50,583] [INFO] Found 6/6 markers.
[2024-01-24 14:05:50,622] [INFO] Query marker FASTA was written to GCF_000830985.1_ASM83098v1_genomic.fna/markers.fasta
[2024-01-24 14:05:50,622] [INFO] Task started: Blastn
[2024-01-24 14:05:50,622] [INFO] Running command: blastn -query GCF_000830985.1_ASM83098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference/reference_markers.fasta -out GCF_000830985.1_ASM83098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:51,447] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:51,520] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:51,520] [INFO] Target genome list was writen to GCF_000830985.1_ASM83098v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:51,540] [INFO] Task started: fastANI
[2024-01-24 14:05:51,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e9c611a-1120-4920-9272-1722234f7b77/GCF_000830985.1_ASM83098v1_genomic.fna.gz --refList GCF_000830985.1_ASM83098v1_genomic.fna/target_genomes.txt --output GCF_000830985.1_ASM83098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,671] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,688] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:07,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:07,688] [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
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	100.0	1325	1325	95	conclusive
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	92.181	1100	1325	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	89.8846	1109	1325	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	81.3489	786	1325	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	80.699	668	1325	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	80.6856	656	1325	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.4345	615	1325	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	80.237	670	1325	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	80.1988	576	1325	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.0815	557	1325	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.7519	561	1325	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	79.7445	455	1325	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.6558	534	1325	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	79.5778	528	1325	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.2935	572	1325	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.9263	453	1325	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.6581	396	1325	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,690] [INFO] DFAST Taxonomy check result was written to GCF_000830985.1_ASM83098v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference/checkm_data
[2024-01-24 14:06:07,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,740] [INFO] Task started: CheckM
[2024-01-24 14:06:07,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000830985.1_ASM83098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000830985.1_ASM83098v1_genomic.fna/checkm_input GCF_000830985.1_ASM83098v1_genomic.fna/checkm_result
[2024-01-24 14:06:48,534] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:48,536] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:48,557] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:48,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:48,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000830985.1_ASM83098v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:48,558] [INFO] Task started: Blastn
[2024-01-24 14:06:48,558] [INFO] Running command: blastn -query GCF_000830985.1_ASM83098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb21716f0-b8e5-4091-855d-9d813d6281b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000830985.1_ASM83098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:49,800] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:49,803] [INFO] Selected 16 target genomes.
[2024-01-24 14:06:49,803] [INFO] Target genome list was writen to GCF_000830985.1_ASM83098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:49,814] [INFO] Task started: fastANI
[2024-01-24 14:06:49,814] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e9c611a-1120-4920-9272-1722234f7b77/GCF_000830985.1_ASM83098v1_genomic.fna.gz --refList GCF_000830985.1_ASM83098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000830985.1_ASM83098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:02,714] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:02,728] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:02,728] [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
GCA_000830985.1	s__Marinobacter similis	100.0	1325	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016820575.1	s__Marinobacter sediminum	92.181	1100	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871205.1	s__Marinobacter alexandrii	89.8846	1109	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_001650915.1	s__Marinobacter sp001650915	80.796	686	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	80.7359	642	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_000166295.1	s__Marinobacter adhaerens	80.699	668	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_002933295.1	s__Marinobacter flavimaris	80.6856	656	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCA_003030785.1	s__Marinobacter sp003030785	80.4556	410	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	80.2511	668	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_002258215.1	s__Marinobacter vinifirmus	80.2016	576	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_900115175.1	s__Marinobacter gudaonensis	80.1457	663	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	80.0326	599	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	79.7329	418	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	79.6961	528	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_001447155.2	s__Marinobacter sp001447155	79.6527	578	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	79.2926	573	1325	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:02,730] [INFO] GTDB search result was written to GCF_000830985.1_ASM83098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:02,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:02,734] [INFO] DFAST_QC result json was written to GCF_000830985.1_ASM83098v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:02,735] [INFO] DFAST_QC completed!
[2024-01-24 14:07:02,735] [INFO] Total running time: 0h1m27s