[2023-03-15 18:39:12,252] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:39:12,252] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:39:12,252] [INFO] DQC Reference Directory: /var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference
[2023-03-15 18:39:13,656] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:39:13,656] [INFO] Task started: Prodigal
[2023-03-15 18:39:13,656] [INFO] Running command: cat /var/lib/cwl/stgf4d40d13-eb80-44e5-bc5e-2a6d01a3637a/OceanDNA-b29618.fa | prodigal -d OceanDNA-b29618/cds.fna -a OceanDNA-b29618/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:39:30,383] [INFO] Task succeeded: Prodigal
[2023-03-15 18:39:30,383] [INFO] Task started: HMMsearch
[2023-03-15 18:39:30,384] [INFO] Running command: hmmsearch --tblout OceanDNA-b29618/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference/reference_markers.hmm OceanDNA-b29618/protein.faa > /dev/null
[2023-03-15 18:39:30,576] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:39:30,576] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf4d40d13-eb80-44e5-bc5e-2a6d01a3637a/OceanDNA-b29618.fa]
[2023-03-15 18:39:30,599] [INFO] Query marker FASTA was written to OceanDNA-b29618/markers.fasta
[2023-03-15 18:39:30,599] [INFO] Task started: Blastn
[2023-03-15 18:39:30,599] [INFO] Running command: blastn -query OceanDNA-b29618/markers.fasta -db /var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference/reference_markers.fasta -out OceanDNA-b29618/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:39:31,228] [INFO] Task succeeded: Blastn
[2023-03-15 18:39:31,228] [INFO] Selected 14 target genomes.
[2023-03-15 18:39:31,229] [INFO] Target genome list was writen to OceanDNA-b29618/target_genomes.txt
[2023-03-15 18:39:31,237] [INFO] Task started: fastANI
[2023-03-15 18:39:31,237] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4d40d13-eb80-44e5-bc5e-2a6d01a3637a/OceanDNA-b29618.fa --refList OceanDNA-b29618/target_genomes.txt --output OceanDNA-b29618/fastani_result.tsv --threads 1
[2023-03-15 18:39:42,049] [INFO] Task succeeded: fastANI
[2023-03-15 18:39:42,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:39:42,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:39:42,059] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2023-03-15 18:39:42,059] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 18:39:42,059] [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
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	98.4578	804	831	95	conclusive
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	98.4578	804	831	95	conclusive
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	98.4284	808	831	95	conclusive
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	81.4714	585	831	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	81.4417	559	831	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	81.4159	569	831	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	81.3679	567	831	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	80.7472	540	831	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	79.7291	435	831	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.8037	347	831	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.4277	196	831	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.2036	223	831	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.7811	224	831	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.4563	97	831	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:39:42,059] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29618/tc_result.tsv
[2023-03-15 18:39:42,059] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:39:42,059] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:39:42,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference/checkm_data
[2023-03-15 18:39:42,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:39:42,065] [INFO] Task started: CheckM
[2023-03-15 18:39:42,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29618/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29618/checkm_input OceanDNA-b29618/checkm_result
[2023-03-15 18:40:26,154] [INFO] Task succeeded: CheckM
[2023-03-15 18:40:26,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.10%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:40:26,156] [INFO] ===== Completeness check finished =====
[2023-03-15 18:40:26,157] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:40:26,157] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29618/markers.fasta)
[2023-03-15 18:40:26,157] [INFO] Task started: Blastn
[2023-03-15 18:40:26,157] [INFO] Running command: blastn -query OceanDNA-b29618/markers.fasta -db /var/lib/cwl/stgd68f4084-0a13-4155-bc59-f0659e9b3cc9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29618/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:40:27,144] [INFO] Task succeeded: Blastn
[2023-03-15 18:40:27,145] [INFO] Selected 14 target genomes.
[2023-03-15 18:40:27,145] [INFO] Target genome list was writen to OceanDNA-b29618/target_genomes_gtdb.txt
[2023-03-15 18:40:27,499] [INFO] Task started: fastANI
[2023-03-15 18:40:27,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4d40d13-eb80-44e5-bc5e-2a6d01a3637a/OceanDNA-b29618.fa --refList OceanDNA-b29618/target_genomes_gtdb.txt --output OceanDNA-b29618/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:40:40,015] [INFO] Task succeeded: fastANI
[2023-03-15 18:40:40,023] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 18:40:40,023] [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_001258055.1	s__Phaeobacter italicus	98.4578	804	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	conclusive
GCF_002407245.1	s__Phaeobacter piscinae	81.4714	585	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	81.4417	559	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_000473105.1	s__Phaeobacter inhibens	81.4282	568	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.82	97.14	0.94	0.90	26	-
GCF_001888185.1	s__Phaeobacter porticola	80.7472	540	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	79.7356	435	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_001458395.1	s__Leisingera aquaemixtae	79.5863	439	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_013317235.1	s__Leisingera sp013317235	79.5256	413	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	79.3527	449	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	79.3286	402	831	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	79.3253	413	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_000813965.1	s__Leisingera sp000813965	79.1983	388	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	79.1162	395	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	78.3064	347	831	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 18:40:40,023] [INFO] GTDB search result was written to OceanDNA-b29618/result_gtdb.tsv
[2023-03-15 18:40:40,024] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:40:40,025] [INFO] DFAST_QC result json was written to OceanDNA-b29618/dqc_result.json
[2023-03-15 18:40:40,025] [INFO] DFAST_QC completed!
[2023-03-15 18:40:40,025] [INFO] Total running time: 0h1m28s