[2023-03-16 16:04:03,639] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:04:03,639] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:04:03,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference
[2023-03-16 16:04:04,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:04:04,926] [INFO] Task started: Prodigal
[2023-03-16 16:04:04,926] [INFO] Running command: cat /var/lib/cwl/stg48bc4dd2-5c7b-4ca2-81ed-ae0f0c2d0637/OceanDNA-b35823.fa | prodigal -d OceanDNA-b35823/cds.fna -a OceanDNA-b35823/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:04:57,057] [INFO] Task succeeded: Prodigal
[2023-03-16 16:04:57,057] [INFO] Task started: HMMsearch
[2023-03-16 16:04:57,058] [INFO] Running command: hmmsearch --tblout OceanDNA-b35823/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference/reference_markers.hmm OceanDNA-b35823/protein.faa > /dev/null
[2023-03-16 16:04:57,471] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:04:57,472] [INFO] Found 6/6 markers.
[2023-03-16 16:04:57,509] [INFO] Query marker FASTA was written to OceanDNA-b35823/markers.fasta
[2023-03-16 16:04:57,510] [INFO] Task started: Blastn
[2023-03-16 16:04:57,510] [INFO] Running command: blastn -query OceanDNA-b35823/markers.fasta -db /var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference/reference_markers.fasta -out OceanDNA-b35823/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:04:58,341] [INFO] Task succeeded: Blastn
[2023-03-16 16:04:58,342] [INFO] Selected 35 target genomes.
[2023-03-16 16:04:58,342] [INFO] Target genome list was writen to OceanDNA-b35823/target_genomes.txt
[2023-03-16 16:04:58,358] [INFO] Task started: fastANI
[2023-03-16 16:04:58,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg48bc4dd2-5c7b-4ca2-81ed-ae0f0c2d0637/OceanDNA-b35823.fa --refList OceanDNA-b35823/target_genomes.txt --output OceanDNA-b35823/fastani_result.tsv --threads 1
[2023-03-16 16:05:28,922] [INFO] Task succeeded: fastANI
[2023-03-16 16:05:28,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:05:28,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:05:28,932] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:05:28,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:05:28,932] [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
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.3287	67	1916	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.2442	66	1916	95	below_threshold
Methyloversatilis universalis	strain=FAM5	GCA_000214035.3	378211	378211	type	True	75.1806	65	1916	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.1421	120	1916	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.1296	72	1916	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.1226	73	1916	95	below_threshold
Trinickia diaoshuihuensis	strain=NEAU-SY24	GCA_003390925.1	2292265	2292265	type	True	75.087	73	1916	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.0774	70	1916	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.0711	60	1916	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.003	60	1916	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	74.971	50	1916	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	74.9306	56	1916	95	below_threshold
Burkholderia latens	strain=CCUG 54555	GCA_008802135.1	488446	488446	suspected-type	True	74.89	135	1916	95	below_threshold
Burkholderia latens		GCA_902499045.1	488446	488446	suspected-type	True	74.8763	140	1916	95	below_threshold
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	74.7268	56	1916	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:05:28,933] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35823/tc_result.tsv
[2023-03-16 16:05:28,933] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:05:28,933] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:05:28,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference/checkm_data
[2023-03-16 16:05:28,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:05:29,004] [INFO] Task started: CheckM
[2023-03-16 16:05:29,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35823/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35823/checkm_input OceanDNA-b35823/checkm_result
[2023-03-16 16:07:03,920] [INFO] Task succeeded: CheckM
[2023-03-16 16:07:03,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:07:03,924] [INFO] ===== Completeness check finished =====
[2023-03-16 16:07:03,924] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:07:03,924] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35823/markers.fasta)
[2023-03-16 16:07:03,926] [INFO] Task started: Blastn
[2023-03-16 16:07:03,926] [INFO] Running command: blastn -query OceanDNA-b35823/markers.fasta -db /var/lib/cwl/stg0154328b-73e0-4b34-8910-f585bd9ae9ef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35823/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:07:05,405] [INFO] Task succeeded: Blastn
[2023-03-16 16:07:05,406] [INFO] Selected 25 target genomes.
[2023-03-16 16:07:05,407] [INFO] Target genome list was writen to OceanDNA-b35823/target_genomes_gtdb.txt
[2023-03-16 16:07:06,401] [INFO] Task started: fastANI
[2023-03-16 16:07:06,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg48bc4dd2-5c7b-4ca2-81ed-ae0f0c2d0637/OceanDNA-b35823.fa --refList OceanDNA-b35823/target_genomes_gtdb.txt --output OceanDNA-b35823/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:07:26,141] [INFO] Task succeeded: fastANI
[2023-03-16 16:07:26,150] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:07:26,150] [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_001464935.1	s__Ga0077536 sp001464935	76.4808	227	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209015.1	s__JACQWY01 sp016209015	76.3197	267	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JACQWY01	95.0	99.49	99.49	0.94	0.94	2	-
GCA_016719885.1	s__JADJYF01 sp016719885	76.0464	231	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
GCA_016191285.1	s__CAIKBL01 sp016191285	75.806	88	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__CAIKBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874535.1	s__CAIKBL01 sp016874535	75.5731	87	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__CAIKBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716465.1	s__JADJWH01 sp016716465	75.356	61	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	75.249	52	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.2088	101	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_016712635.1	s__JADJWH01 sp016712635	75.1385	60	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182095.1	s__Plasticicumulans acidivorans	75.0702	71	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004327335.1	s__Pseudomonas_Q kirkiae	75.0571	58	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	99.65	99.41	0.96	0.94	4	-
GCF_003050935.1	s__Luteibacter sp003050935	75.0062	53	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	74.9541	84	1916	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:07:26,150] [INFO] GTDB search result was written to OceanDNA-b35823/result_gtdb.tsv
[2023-03-16 16:07:26,151] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:07:26,152] [INFO] DFAST_QC result json was written to OceanDNA-b35823/dqc_result.json
[2023-03-16 16:07:26,152] [INFO] DFAST_QC completed!
[2023-03-16 16:07:26,152] [INFO] Total running time: 0h3m23s