[2023-03-16 15:11:23,462] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:11:23,462] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:11:23,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference
[2023-03-16 15:11:24,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:11:24,899] [INFO] Task started: Prodigal
[2023-03-16 15:11:24,899] [INFO] Running command: cat /var/lib/cwl/stg3a722fba-ca69-43ca-82a5-14e95a6cd3eb/OceanDNA-b10094.fa | prodigal -d OceanDNA-b10094/cds.fna -a OceanDNA-b10094/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:11:40,503] [INFO] Task succeeded: Prodigal
[2023-03-16 15:11:40,503] [INFO] Task started: HMMsearch
[2023-03-16 15:11:40,503] [INFO] Running command: hmmsearch --tblout OceanDNA-b10094/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference/reference_markers.hmm OceanDNA-b10094/protein.faa > /dev/null
[2023-03-16 15:11:40,678] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:11:40,679] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3a722fba-ca69-43ca-82a5-14e95a6cd3eb/OceanDNA-b10094.fa]
[2023-03-16 15:11:40,697] [INFO] Query marker FASTA was written to OceanDNA-b10094/markers.fasta
[2023-03-16 15:11:40,697] [INFO] Task started: Blastn
[2023-03-16 15:11:40,698] [INFO] Running command: blastn -query OceanDNA-b10094/markers.fasta -db /var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference/reference_markers.fasta -out OceanDNA-b10094/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:11:41,199] [INFO] Task succeeded: Blastn
[2023-03-16 15:11:41,200] [INFO] Selected 16 target genomes.
[2023-03-16 15:11:41,200] [INFO] Target genome list was writen to OceanDNA-b10094/target_genomes.txt
[2023-03-16 15:11:41,214] [INFO] Task started: fastANI
[2023-03-16 15:11:41,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a722fba-ca69-43ca-82a5-14e95a6cd3eb/OceanDNA-b10094.fa --refList OceanDNA-b10094/target_genomes.txt --output OceanDNA-b10094/fastani_result.tsv --threads 1
[2023-03-16 15:11:54,707] [INFO] Task succeeded: fastANI
[2023-03-16 15:11:54,707] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:11:54,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:11:54,717] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:11:54,717] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:11:54,717] [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
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	78.3313	330	788	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	78.0485	301	788	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.7711	279	788	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.439	175	788	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.1302	192	788	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	77.1214	214	788	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	77.1055	202	788	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.8886	151	788	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.6584	128	788	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	76.6512	126	788	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	76.6228	125	788	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.4383	135	788	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.3301	121	788	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.2762	108	788	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.2347	122	788	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	75.9587	108	788	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:11:54,717] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10094/tc_result.tsv
[2023-03-16 15:11:54,717] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:11:54,717] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:11:54,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference/checkm_data
[2023-03-16 15:11:54,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:11:54,730] [INFO] Task started: CheckM
[2023-03-16 15:11:54,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10094/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10094/checkm_input OceanDNA-b10094/checkm_result
[2023-03-16 15:12:54,182] [INFO] Task succeeded: CheckM
[2023-03-16 15:12:54,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:12:54,205] [INFO] ===== Completeness check finished =====
[2023-03-16 15:12:54,205] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:12:54,205] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10094/markers.fasta)
[2023-03-16 15:12:54,205] [INFO] Task started: Blastn
[2023-03-16 15:12:54,205] [INFO] Running command: blastn -query OceanDNA-b10094/markers.fasta -db /var/lib/cwl/stg0d70f5c4-c0ce-404c-9410-10e0e322b2ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10094/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:12:54,891] [INFO] Task succeeded: Blastn
[2023-03-16 15:12:54,891] [INFO] Selected 8 target genomes.
[2023-03-16 15:12:54,892] [INFO] Target genome list was writen to OceanDNA-b10094/target_genomes_gtdb.txt
[2023-03-16 15:12:55,017] [INFO] Task started: fastANI
[2023-03-16 15:12:55,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a722fba-ca69-43ca-82a5-14e95a6cd3eb/OceanDNA-b10094.fa --refList OceanDNA-b10094/target_genomes_gtdb.txt --output OceanDNA-b10094/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:13:01,764] [INFO] Task succeeded: fastANI
[2023-03-16 15:13:01,769] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:13:01,770] [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_000425305.1	s__Psychroserpens burtonensis	83.9087	609	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
GCA_905479815.1	s__Psychroserpens sp905479815	83.3173	525	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	82.41	588	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826655.1	s__Psychroserpens damuponensis	80.5865	510	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799465.1	s__Psychroserpens sp000799465	79.2521	419	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	78.0485	301	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	76.9835	183	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	76.8886	151	788	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:13:01,770] [INFO] GTDB search result was written to OceanDNA-b10094/result_gtdb.tsv
[2023-03-16 15:13:01,770] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:13:01,771] [INFO] DFAST_QC result json was written to OceanDNA-b10094/dqc_result.json
[2023-03-16 15:13:01,772] [INFO] DFAST_QC completed!
[2023-03-16 15:13:01,772] [INFO] Total running time: 0h1m38s