[2023-03-18 06:30:24,838] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:30:24,839] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:30:24,839] [INFO] DQC Reference Directory: /var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference
[2023-03-18 06:30:25,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:30:25,936] [INFO] Task started: Prodigal
[2023-03-18 06:30:25,937] [INFO] Running command: cat /var/lib/cwl/stgc28a8376-ff72-4445-b162-5c008893955b/OceanDNA-b28238.fa | prodigal -d OceanDNA-b28238/cds.fna -a OceanDNA-b28238/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:30:37,869] [INFO] Task succeeded: Prodigal
[2023-03-18 06:30:37,869] [INFO] Task started: HMMsearch
[2023-03-18 06:30:37,869] [INFO] Running command: hmmsearch --tblout OceanDNA-b28238/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference/reference_markers.hmm OceanDNA-b28238/protein.faa > /dev/null
[2023-03-18 06:30:38,041] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:30:38,041] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc28a8376-ff72-4445-b162-5c008893955b/OceanDNA-b28238.fa]
[2023-03-18 06:30:38,072] [INFO] Query marker FASTA was written to OceanDNA-b28238/markers.fasta
[2023-03-18 06:30:38,072] [INFO] Task started: Blastn
[2023-03-18 06:30:38,072] [INFO] Running command: blastn -query OceanDNA-b28238/markers.fasta -db /var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference/reference_markers.fasta -out OceanDNA-b28238/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:30:38,687] [INFO] Task succeeded: Blastn
[2023-03-18 06:30:38,689] [INFO] Selected 12 target genomes.
[2023-03-18 06:30:38,690] [INFO] Target genome list was writen to OceanDNA-b28238/target_genomes.txt
[2023-03-18 06:30:38,757] [INFO] Task started: fastANI
[2023-03-18 06:30:38,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28a8376-ff72-4445-b162-5c008893955b/OceanDNA-b28238.fa --refList OceanDNA-b28238/target_genomes.txt --output OceanDNA-b28238/fastani_result.tsv --threads 1
[2023-03-18 06:30:47,351] [INFO] Task succeeded: fastANI
[2023-03-18 06:30:47,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:30:47,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:30:47,360] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:30:47,360] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:30:47,360] [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 caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	80.1149	266	544	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	79.8276	291	544	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	79.7876	286	544	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	79.3228	256	544	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	79.2576	262	544	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	78.2036	185	544	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.589	154	544	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.9214	91	544	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.9167	151	544	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8302	95	544	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.5874	98	544	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.4748	84	544	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:30:47,363] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28238/tc_result.tsv
[2023-03-18 06:30:47,368] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:30:47,368] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:30:47,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference/checkm_data
[2023-03-18 06:30:47,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:30:47,394] [INFO] Task started: CheckM
[2023-03-18 06:30:47,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28238/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28238/checkm_input OceanDNA-b28238/checkm_result
[2023-03-18 06:31:21,142] [INFO] Task succeeded: CheckM
[2023-03-18 06:31:21,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:31:21,158] [INFO] ===== Completeness check finished =====
[2023-03-18 06:31:21,158] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:31:21,158] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28238/markers.fasta)
[2023-03-18 06:31:21,160] [INFO] Task started: Blastn
[2023-03-18 06:31:21,160] [INFO] Running command: blastn -query OceanDNA-b28238/markers.fasta -db /var/lib/cwl/stge8600fd6-6c60-4324-8db7-f9a8e6f4204b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28238/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:31:22,112] [INFO] Task succeeded: Blastn
[2023-03-18 06:31:22,115] [INFO] Selected 10 target genomes.
[2023-03-18 06:31:22,115] [INFO] Target genome list was writen to OceanDNA-b28238/target_genomes_gtdb.txt
[2023-03-18 06:31:22,141] [INFO] Task started: fastANI
[2023-03-18 06:31:22,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgc28a8376-ff72-4445-b162-5c008893955b/OceanDNA-b28238.fa --refList OceanDNA-b28238/target_genomes_gtdb.txt --output OceanDNA-b28238/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:31:29,695] [INFO] Task succeeded: fastANI
[2023-03-18 06:31:29,701] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:31:29,702] [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_900143635.1	s__FREY01 sp900143635	82.5141	371	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__FREY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	80.1267	265	544	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	79.8558	289	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000203975.2	s__Leisingera sp000203975	79.83	283	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_000473145.1	s__Leisingera daeponensis	79.8141	285	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_013317235.1	s__Leisingera sp013317235	79.7548	282	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	79.5982	278	544	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	79.5366	280	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	79.312	257	544	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	79.2941	260	544	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 06:31:29,703] [INFO] GTDB search result was written to OceanDNA-b28238/result_gtdb.tsv
[2023-03-18 06:31:29,704] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:31:29,707] [INFO] DFAST_QC result json was written to OceanDNA-b28238/dqc_result.json
[2023-03-18 06:31:29,707] [INFO] DFAST_QC completed!
[2023-03-18 06:31:29,707] [INFO] Total running time: 0h1m5s