[2024-01-25 18:47:05,854] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:05,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:05,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference
[2024-01-25 18:47:07,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:07,003] [INFO] Task started: Prodigal
[2024-01-25 18:47:07,004] [INFO] Running command: gunzip -c /var/lib/cwl/stgded20e11-3748-4e4d-8af4-f81e2aacc398/GCF_004006175.1_ASM400617v1_genomic.fna.gz | prodigal -d GCF_004006175.1_ASM400617v1_genomic.fna/cds.fna -a GCF_004006175.1_ASM400617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:21,250] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:21,251] [INFO] Task started: HMMsearch
[2024-01-25 18:47:21,251] [INFO] Running command: hmmsearch --tblout GCF_004006175.1_ASM400617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference/reference_markers.hmm GCF_004006175.1_ASM400617v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:21,581] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:21,582] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgded20e11-3748-4e4d-8af4-f81e2aacc398/GCF_004006175.1_ASM400617v1_genomic.fna.gz]
[2024-01-25 18:47:21,628] [INFO] Query marker FASTA was written to GCF_004006175.1_ASM400617v1_genomic.fna/markers.fasta
[2024-01-25 18:47:21,628] [INFO] Task started: Blastn
[2024-01-25 18:47:21,629] [INFO] Running command: blastn -query GCF_004006175.1_ASM400617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference/reference_markers.fasta -out GCF_004006175.1_ASM400617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:22,351] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:22,354] [INFO] Selected 15 target genomes.
[2024-01-25 18:47:22,354] [INFO] Target genome list was writen to GCF_004006175.1_ASM400617v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:22,366] [INFO] Task started: fastANI
[2024-01-25 18:47:22,366] [INFO] Running command: fastANI --query /var/lib/cwl/stgded20e11-3748-4e4d-8af4-f81e2aacc398/GCF_004006175.1_ASM400617v1_genomic.fna.gz --refList GCF_004006175.1_ASM400617v1_genomic.fna/target_genomes.txt --output GCF_004006175.1_ASM400617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:34,384] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:34,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:34,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:34,395] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:47:34,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:47:34,395] [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
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	80.746	768	1691	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	80.6746	756	1691	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	78.5917	487	1691	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	78.3812	457	1691	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.167	466	1691	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.1585	407	1691	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	78.1185	373	1691	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.0557	397	1691	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.022	463	1691	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	77.96	401	1691	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	77.8178	392	1691	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.6519	367	1691	95	below_threshold
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	77.517	266	1691	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.5993	136	1691	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.4953	185	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:34,397] [INFO] DFAST Taxonomy check result was written to GCF_004006175.1_ASM400617v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:34,397] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:34,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:34,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference/checkm_data
[2024-01-25 18:47:34,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:34,447] [INFO] Task started: CheckM
[2024-01-25 18:47:34,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004006175.1_ASM400617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004006175.1_ASM400617v1_genomic.fna/checkm_input GCF_004006175.1_ASM400617v1_genomic.fna/checkm_result
[2024-01-25 18:48:17,355] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:17,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:17,375] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:17,375] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:17,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004006175.1_ASM400617v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:17,377] [INFO] Task started: Blastn
[2024-01-25 18:48:17,377] [INFO] Running command: blastn -query GCF_004006175.1_ASM400617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72c3424b-388b-4c09-a184-a9069dbcff80/dqc_reference/reference_markers_gtdb.fasta -out GCF_004006175.1_ASM400617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:18,564] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:18,571] [INFO] Selected 7 target genomes.
[2024-01-25 18:48:18,571] [INFO] Target genome list was writen to GCF_004006175.1_ASM400617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:18,604] [INFO] Task started: fastANI
[2024-01-25 18:48:18,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgded20e11-3748-4e4d-8af4-f81e2aacc398/GCF_004006175.1_ASM400617v1_genomic.fna.gz --refList GCF_004006175.1_ASM400617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004006175.1_ASM400617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:26,164] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:26,169] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:26,169] [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_004006175.1	s__Parasedimentitalea marina	100.0	1691	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013214575.1	s__Parasedimentitalea sp013214575	83.4841	1003	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011813015.1	s__Parasedimentitalea sp011813015	81.6239	910	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162795.1	s__Parasedimentitalea sp002162795	81.1663	890	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401945.1	s__Parasedimentitalea sp002401945	80.9879	804	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753675.1	s__Parasedimentitalea huanghaiensis	80.7355	769	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771405.1	s__Parasedimentitalea marina_A	80.6665	757	1691	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:26,171] [INFO] GTDB search result was written to GCF_004006175.1_ASM400617v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:26,171] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:26,175] [INFO] DFAST_QC result json was written to GCF_004006175.1_ASM400617v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:26,175] [INFO] DFAST_QC completed!
[2024-01-25 18:48:26,175] [INFO] Total running time: 0h1m20s