[2023-03-16 23:05:03,948] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,948] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,949] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference
[2023-03-16 23:05:05,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,362] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,362] [INFO] Running command: cat /var/lib/cwl/stg570d45ff-6d95-4498-96c4-bda8892dc448/OceanDNA-b4498.fa | prodigal -d OceanDNA-b4498/cds.fna -a OceanDNA-b4498/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:42,224] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:42,225] [INFO] Task started: HMMsearch
[2023-03-16 23:05:42,225] [INFO] Running command: hmmsearch --tblout OceanDNA-b4498/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference/reference_markers.hmm OceanDNA-b4498/protein.faa > /dev/null
[2023-03-16 23:05:42,492] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:42,492] [INFO] Found 6/6 markers.
[2023-03-16 23:05:42,524] [INFO] Query marker FASTA was written to OceanDNA-b4498/markers.fasta
[2023-03-16 23:05:42,524] [INFO] Task started: Blastn
[2023-03-16 23:05:42,524] [INFO] Running command: blastn -query OceanDNA-b4498/markers.fasta -db /var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference/reference_markers.fasta -out OceanDNA-b4498/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:43,066] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:43,066] [INFO] Selected 23 target genomes.
[2023-03-16 23:05:43,067] [INFO] Target genome list was writen to OceanDNA-b4498/target_genomes.txt
[2023-03-16 23:05:43,078] [INFO] Task started: fastANI
[2023-03-16 23:05:43,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg570d45ff-6d95-4498-96c4-bda8892dc448/OceanDNA-b4498.fa --refList OceanDNA-b4498/target_genomes.txt --output OceanDNA-b4498/fastani_result.tsv --threads 1
[2023-03-16 23:06:01,198] [INFO] Task succeeded: fastANI
[2023-03-16 23:06:01,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:06:01,199] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:06:01,204] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:06:01,204] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:06:01,204] [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
Emticicia aquatica	strain=CECT 8858, type strain	GCA_923079645.1	1681835	1681835	type	True	80.3321	945	1718	95	below_threshold
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	80.2392	1007	1718	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	76.5461	277	1718	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	76.4373	116	1718	95	below_threshold
Arcicella aurantiaca	strain=DSM 22214	GCA_003148625.1	591202	591202	type	True	76.325	195	1718	95	below_threshold
Flectobacillus major	strain=DSM 103	GCA_000427405.1	103	103	type	True	75.8772	106	1718	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:06:01,204] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4498/tc_result.tsv
[2023-03-16 23:06:01,204] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:06:01,204] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:06:01,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference/checkm_data
[2023-03-16 23:06:01,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:06:01,278] [INFO] Task started: CheckM
[2023-03-16 23:06:01,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4498/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4498/checkm_input OceanDNA-b4498/checkm_result
[2023-03-16 23:07:29,316] [INFO] Task succeeded: CheckM
[2023-03-16 23:07:29,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:07:29,319] [INFO] ===== Completeness check finished =====
[2023-03-16 23:07:29,319] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:07:29,319] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4498/markers.fasta)
[2023-03-16 23:07:29,320] [INFO] Task started: Blastn
[2023-03-16 23:07:29,320] [INFO] Running command: blastn -query OceanDNA-b4498/markers.fasta -db /var/lib/cwl/stgbf600452-8afd-474e-b4cf-f664b6ae3970/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4498/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:07:30,034] [INFO] Task succeeded: Blastn
[2023-03-16 23:07:30,034] [INFO] Selected 18 target genomes.
[2023-03-16 23:07:30,034] [INFO] Target genome list was writen to OceanDNA-b4498/target_genomes_gtdb.txt
[2023-03-16 23:07:30,505] [INFO] Task started: fastANI
[2023-03-16 23:07:30,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg570d45ff-6d95-4498-96c4-bda8892dc448/OceanDNA-b4498.fa --refList OceanDNA-b4498/target_genomes_gtdb.txt --output OceanDNA-b4498/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:07:45,678] [INFO] Task succeeded: fastANI
[2023-03-16 23:07:45,685] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:07:45,685] [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_017495105.1	s__Emticicia sp017495105	80.3002	786	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644295.1	s__Emticicia aquatilis	80.2392	1007	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000263195.1	s__Emticicia oligotrophica	78.5036	731	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013912375.1	s__Emticicia sp013912375	76.5631	274	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168285.1	s__Emticicia sp004168285	76.5461	277	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003418935.1	s__Emticicia sp003418935	76.2604	266	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204325.1	s__Arcicella rosea	76.0065	148	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arcicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298025.1	s__Flectobacillus sp013298025	75.9888	94	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Flectobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256295.1	s__Leadbetterella sp002256295	75.9565	103	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	97.02	97.02	0.83	0.83	2	-
GCA_900230115.1	s__TFI-002 sp900230115	75.4054	65	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__TFI-002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298075.1	s__RDXZ01 sp013298075	75.0466	85	1718	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Microscillaceae;g__RDXZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:07:45,686] [INFO] GTDB search result was written to OceanDNA-b4498/result_gtdb.tsv
[2023-03-16 23:07:45,686] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:07:45,687] [INFO] DFAST_QC result json was written to OceanDNA-b4498/dqc_result.json
[2023-03-16 23:07:45,687] [INFO] DFAST_QC completed!
[2023-03-16 23:07:45,687] [INFO] Total running time: 0h2m42s