[2023-03-18 04:04:53,883] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:04:53,883] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:04:53,883] [INFO] DQC Reference Directory: /var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference
[2023-03-18 04:04:55,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:04:55,026] [INFO] Task started: Prodigal
[2023-03-18 04:04:55,026] [INFO] Running command: cat /var/lib/cwl/stg8f8935b4-6ee1-4b54-bc64-6348c6ef526b/OceanDNA-b29408.fa | prodigal -d OceanDNA-b29408/cds.fna -a OceanDNA-b29408/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:05:22,731] [INFO] Task succeeded: Prodigal
[2023-03-18 04:05:22,732] [INFO] Task started: HMMsearch
[2023-03-18 04:05:22,732] [INFO] Running command: hmmsearch --tblout OceanDNA-b29408/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference/reference_markers.hmm OceanDNA-b29408/protein.faa > /dev/null
[2023-03-18 04:05:22,945] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:05:22,946] [INFO] Found 6/6 markers.
[2023-03-18 04:05:22,972] [INFO] Query marker FASTA was written to OceanDNA-b29408/markers.fasta
[2023-03-18 04:05:22,973] [INFO] Task started: Blastn
[2023-03-18 04:05:22,973] [INFO] Running command: blastn -query OceanDNA-b29408/markers.fasta -db /var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference/reference_markers.fasta -out OceanDNA-b29408/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:05:23,807] [INFO] Task succeeded: Blastn
[2023-03-18 04:05:23,808] [INFO] Selected 10 target genomes.
[2023-03-18 04:05:23,808] [INFO] Target genome list was writen to OceanDNA-b29408/target_genomes.txt
[2023-03-18 04:05:23,841] [INFO] Task started: fastANI
[2023-03-18 04:05:23,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8935b4-6ee1-4b54-bc64-6348c6ef526b/OceanDNA-b29408.fa --refList OceanDNA-b29408/target_genomes.txt --output OceanDNA-b29408/fastani_result.tsv --threads 1
[2023-03-18 04:05:33,498] [INFO] Task succeeded: fastANI
[2023-03-18 04:05:33,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:05:33,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:05:33,506] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:05:33,506] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:05:33,506] [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
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	99.0283	1383	1435	95	conclusive
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	88.3949	1138	1435	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	85.9708	1129	1435	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	85.8413	1147	1435	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	85.5967	1089	1435	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	78.5532	568	1435	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.5108	339	1435	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.4746	294	1435	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3243	292	1435	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2879	250	1435	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:05:33,507] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29408/tc_result.tsv
[2023-03-18 04:05:33,507] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:05:33,508] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:05:33,508] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference/checkm_data
[2023-03-18 04:05:33,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:05:33,516] [INFO] Task started: CheckM
[2023-03-18 04:05:33,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29408/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29408/checkm_input OceanDNA-b29408/checkm_result
[2023-03-18 04:06:40,481] [INFO] Task succeeded: CheckM
[2023-03-18 04:06:40,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:06:40,500] [INFO] ===== Completeness check finished =====
[2023-03-18 04:06:40,500] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:06:40,500] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29408/markers.fasta)
[2023-03-18 04:06:40,501] [INFO] Task started: Blastn
[2023-03-18 04:06:40,502] [INFO] Running command: blastn -query OceanDNA-b29408/markers.fasta -db /var/lib/cwl/stga3f7c3f2-98c9-4ea0-b2d6-de4b6a45f68b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29408/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:06:41,982] [INFO] Task succeeded: Blastn
[2023-03-18 04:06:41,983] [INFO] Selected 10 target genomes.
[2023-03-18 04:06:41,983] [INFO] Target genome list was writen to OceanDNA-b29408/target_genomes_gtdb.txt
[2023-03-18 04:06:42,127] [INFO] Task started: fastANI
[2023-03-18 04:06:42,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f8935b4-6ee1-4b54-bc64-6348c6ef526b/OceanDNA-b29408.fa --refList OceanDNA-b29408/target_genomes_gtdb.txt --output OceanDNA-b29408/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:06:54,355] [INFO] Task succeeded: fastANI
[2023-03-18 04:06:54,361] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:06:54,361] [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_000473165.1	s__Leisingera aquimarina	99.0283	1383	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004123675.1	s__Leisingera sp004123675	90.6411	1253	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_000511355.1	s__Leisingera methylohalidivorans	88.3807	1140	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	85.994	1126	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000473325.1	s__Leisingera caerulea	85.8422	1146	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	85.6267	1123	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_013317235.1	s__Leisingera sp013317235	85.6238	1103	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	85.5807	1091	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_001679925.1	s__Leisingera sp001679925	85.3742	1110	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	85.1761	1086	1435	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:06:54,363] [INFO] GTDB search result was written to OceanDNA-b29408/result_gtdb.tsv
[2023-03-18 04:06:54,363] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:06:54,365] [INFO] DFAST_QC result json was written to OceanDNA-b29408/dqc_result.json
[2023-03-18 04:06:54,365] [INFO] DFAST_QC completed!
[2023-03-18 04:06:54,365] [INFO] Total running time: 0h2m0s