[2024-01-25 18:02:50,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:50,613] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:50,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference
[2024-01-25 18:02:51,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:51,745] [INFO] Task started: Prodigal
[2024-01-25 18:02:51,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a58442b-9682-4edc-b1de-6f432f647577/GCF_002105285.1_ASM210528v1_genomic.fna.gz | prodigal -d GCF_002105285.1_ASM210528v1_genomic.fna/cds.fna -a GCF_002105285.1_ASM210528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:02,354] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:02,354] [INFO] Task started: HMMsearch
[2024-01-25 18:03:02,354] [INFO] Running command: hmmsearch --tblout GCF_002105285.1_ASM210528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference/reference_markers.hmm GCF_002105285.1_ASM210528v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:02,555] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:02,557] [INFO] Found 6/6 markers.
[2024-01-25 18:03:02,587] [INFO] Query marker FASTA was written to GCF_002105285.1_ASM210528v1_genomic.fna/markers.fasta
[2024-01-25 18:03:02,587] [INFO] Task started: Blastn
[2024-01-25 18:03:02,587] [INFO] Running command: blastn -query GCF_002105285.1_ASM210528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference/reference_markers.fasta -out GCF_002105285.1_ASM210528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:03,227] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:03,231] [INFO] Selected 22 target genomes.
[2024-01-25 18:03:03,231] [INFO] Target genome list was writen to GCF_002105285.1_ASM210528v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:03,248] [INFO] Task started: fastANI
[2024-01-25 18:03:03,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a58442b-9682-4edc-b1de-6f432f647577/GCF_002105285.1_ASM210528v1_genomic.fna.gz --refList GCF_002105285.1_ASM210528v1_genomic.fna/target_genomes.txt --output GCF_002105285.1_ASM210528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:18,000] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:18,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:18,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:18,014] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:18,014] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:18,014] [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
Planktotalea arctica	strain=IMCC9565	GCA_002105285.1	1481893	1481893	type	True	100.0	1234	1237	95	conclusive
Planktotalea frisia	strain=SH6-1	GCA_001890925.1	696762	696762	type	True	79.4078	523	1237	95	below_threshold
Planktotalea frisia	strain=DSM 23709	GCA_003254185.1	696762	696762	type	True	79.3234	525	1237	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.2821	122	1237	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.093	185	1237	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.0638	238	1237	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	77.0425	138	1237	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.013	184	1237	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.0063	141	1237	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.9859	229	1237	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.9808	220	1237	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.9069	205	1237	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.8123	225	1237	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7945	172	1237	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	76.7199	218	1237	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.717	208	1237	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	76.5192	160	1237	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	76.5124	219	1237	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.4466	208	1237	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.4352	212	1237	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.2665	110	1237	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.2339	93	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:18,016] [INFO] DFAST Taxonomy check result was written to GCF_002105285.1_ASM210528v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:18,016] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:18,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:18,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference/checkm_data
[2024-01-25 18:03:18,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:18,055] [INFO] Task started: CheckM
[2024-01-25 18:03:18,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002105285.1_ASM210528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002105285.1_ASM210528v1_genomic.fna/checkm_input GCF_002105285.1_ASM210528v1_genomic.fna/checkm_result
[2024-01-25 18:03:51,779] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:51,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:51,809] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:51,809] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:51,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002105285.1_ASM210528v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:51,810] [INFO] Task started: Blastn
[2024-01-25 18:03:51,810] [INFO] Running command: blastn -query GCF_002105285.1_ASM210528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27ef015d-c7d8-4100-ab59-e1d3b961f09f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002105285.1_ASM210528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:52,906] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:52,911] [INFO] Selected 13 target genomes.
[2024-01-25 18:03:52,911] [INFO] Target genome list was writen to GCF_002105285.1_ASM210528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:52,921] [INFO] Task started: fastANI
[2024-01-25 18:03:52,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a58442b-9682-4edc-b1de-6f432f647577/GCF_002105285.1_ASM210528v1_genomic.fna.gz --refList GCF_002105285.1_ASM210528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002105285.1_ASM210528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:01,943] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:01,952] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:01,952] [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_002105285.1	s__Planktotalea arctica	100.0	1234	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001890925.1	s__Planktotalea frisia	79.4074	523	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	-
GCA_018607965.1	s__Planktotalea sp018607965	78.7406	410	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000156115.1	s__Planktotalea sp000156115	78.6591	522	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.77	99.74	0.95	0.90	3	-
GCA_018607995.1	s__Planktotalea sp018607995	78.4469	428	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342065.1	s__Primorskyibacter sedentarius	76.9808	220	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.8574	206	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	76.7242	230	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458295.1	s__Ruegeria denitrificans	76.6404	167	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	76.6394	186	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172255.1	s__Roseovarius halotolerans	76.4466	208	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002400675.1	s__NORP181 sp002400675	76.2809	98	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__NORP181	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	76.2524	156	1237	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:01,953] [INFO] GTDB search result was written to GCF_002105285.1_ASM210528v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:01,954] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:01,957] [INFO] DFAST_QC result json was written to GCF_002105285.1_ASM210528v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:01,957] [INFO] DFAST_QC completed!
[2024-01-25 18:04:01,957] [INFO] Total running time: 0h1m11s