[2023-03-15 16:50:18,078] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:50:18,080] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:50:18,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference
[2023-03-15 16:50:19,845] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:50:19,846] [INFO] Task started: Prodigal
[2023-03-15 16:50:19,846] [INFO] Running command: cat /var/lib/cwl/stgb6b1fcda-83ff-473a-89e9-e32aa73cdc87/OceanDNA-a3037.fa | prodigal -d OceanDNA-a3037/cds.fna -a OceanDNA-a3037/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:50:32,307] [INFO] Task succeeded: Prodigal
[2023-03-15 16:50:32,307] [INFO] Task started: HMMsearch
[2023-03-15 16:50:32,307] [INFO] Running command: hmmsearch --tblout OceanDNA-a3037/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference/reference_markers.hmm OceanDNA-a3037/protein.faa > /dev/null
[2023-03-15 16:50:32,478] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:50:32,479] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb6b1fcda-83ff-473a-89e9-e32aa73cdc87/OceanDNA-a3037.fa]
[2023-03-15 16:50:32,504] [INFO] Query marker FASTA was written to OceanDNA-a3037/markers.fasta
[2023-03-15 16:50:32,506] [INFO] Task started: Blastn
[2023-03-15 16:50:32,506] [INFO] Running command: blastn -query OceanDNA-a3037/markers.fasta -db /var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference/reference_markers.fasta -out OceanDNA-a3037/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:50:33,051] [INFO] Task succeeded: Blastn
[2023-03-15 16:50:33,062] [INFO] Selected 5 target genomes.
[2023-03-15 16:50:33,062] [INFO] Target genome list was writen to OceanDNA-a3037/target_genomes.txt
[2023-03-15 16:50:33,066] [INFO] Task started: fastANI
[2023-03-15 16:50:33,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b1fcda-83ff-473a-89e9-e32aa73cdc87/OceanDNA-a3037.fa --refList OceanDNA-a3037/target_genomes.txt --output OceanDNA-a3037/fastani_result.tsv --threads 1
[2023-03-15 16:50:35,884] [INFO] Task succeeded: fastANI
[2023-03-15 16:50:35,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:50:35,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:50:35,885] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:50:35,885] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:50:35,885] [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
--------------------------------------------------------------------------------
[2023-03-15 16:50:35,887] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3037/tc_result.tsv
[2023-03-15 16:50:35,890] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:50:35,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:50:35,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference/checkm_data
[2023-03-15 16:50:35,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:50:35,919] [INFO] Task started: CheckM
[2023-03-15 16:50:35,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3037/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3037/checkm_input OceanDNA-a3037/checkm_result
[2023-03-15 16:51:13,783] [INFO] Task succeeded: CheckM
[2023-03-15 16:51:13,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:51:13,815] [INFO] ===== Completeness check finished =====
[2023-03-15 16:51:13,815] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:51:13,816] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3037/markers.fasta)
[2023-03-15 16:51:13,818] [INFO] Task started: Blastn
[2023-03-15 16:51:13,819] [INFO] Running command: blastn -query OceanDNA-a3037/markers.fasta -db /var/lib/cwl/stg0a245756-dfc5-4061-8789-13c0ffd3937d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3037/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:51:14,487] [INFO] Task succeeded: Blastn
[2023-03-15 16:51:14,492] [INFO] Selected 10 target genomes.
[2023-03-15 16:51:14,492] [INFO] Target genome list was writen to OceanDNA-a3037/target_genomes_gtdb.txt
[2023-03-15 16:51:14,553] [INFO] Task started: fastANI
[2023-03-15 16:51:14,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6b1fcda-83ff-473a-89e9-e32aa73cdc87/OceanDNA-a3037.fa --refList OceanDNA-a3037/target_genomes_gtdb.txt --output OceanDNA-a3037/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:51:18,223] [INFO] Task succeeded: fastANI
[2023-03-15 16:51:18,229] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:51:18,229] [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_002505405.1	s__Poseidonia alphae	99.8968	582	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.19	99.15	0.93	0.90	5	conclusive
GCA_018662715.1	s__Poseidonia sp018662715	82.3397	363	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.82	98.76	0.75	0.74	3	-
GCA_013329255.1	s__MGIIa-L1 sp9513u	77.896	59	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_018662825.1	s__MGIIa-L1 sp018662825	77.2025	52	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
GCA_002714305.1	s__Poseidonia sp002714305	77.0499	95	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_018691345.1	s__MGIIa-L1 sp018691345	76.9438	56	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937025.1	s__MGIIa-L1 sp009937025	76.9074	58	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499705.1	s__MGIIa-L1 sp002499705	76.5619	51	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182635.1	s__MGIIa-L1 sp905182635	76.4839	50	632	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:51:18,236] [INFO] GTDB search result was written to OceanDNA-a3037/result_gtdb.tsv
[2023-03-15 16:51:18,245] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:51:18,254] [INFO] DFAST_QC result json was written to OceanDNA-a3037/dqc_result.json
[2023-03-15 16:51:18,254] [INFO] DFAST_QC completed!
[2023-03-15 16:51:18,254] [INFO] Total running time: 0h1m0s