[2023-03-19 00:44:19,965] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:44:19,965] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:44:19,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference
[2023-03-19 00:44:21,086] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:44:21,087] [INFO] Task started: Prodigal
[2023-03-19 00:44:21,087] [INFO] Running command: cat /var/lib/cwl/stga955fd7f-7348-4db9-a8d6-508d6b226df6/OceanDNA-a3142.fa | prodigal -d OceanDNA-a3142/cds.fna -a OceanDNA-a3142/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:44:32,733] [INFO] Task succeeded: Prodigal
[2023-03-19 00:44:32,733] [INFO] Task started: HMMsearch
[2023-03-19 00:44:32,734] [INFO] Running command: hmmsearch --tblout OceanDNA-a3142/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference/reference_markers.hmm OceanDNA-a3142/protein.faa > /dev/null
[2023-03-19 00:44:32,896] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:44:32,896] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga955fd7f-7348-4db9-a8d6-508d6b226df6/OceanDNA-a3142.fa]
[2023-03-19 00:44:32,910] [INFO] Query marker FASTA was written to OceanDNA-a3142/markers.fasta
[2023-03-19 00:44:32,911] [INFO] Task started: Blastn
[2023-03-19 00:44:32,911] [INFO] Running command: blastn -query OceanDNA-a3142/markers.fasta -db /var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference/reference_markers.fasta -out OceanDNA-a3142/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:44:33,341] [INFO] Task succeeded: Blastn
[2023-03-19 00:44:33,342] [INFO] Selected 4 target genomes.
[2023-03-19 00:44:33,342] [INFO] Target genome list was writen to OceanDNA-a3142/target_genomes.txt
[2023-03-19 00:44:33,345] [INFO] Task started: fastANI
[2023-03-19 00:44:33,345] [INFO] Running command: fastANI --query /var/lib/cwl/stga955fd7f-7348-4db9-a8d6-508d6b226df6/OceanDNA-a3142.fa --refList OceanDNA-a3142/target_genomes.txt --output OceanDNA-a3142/fastani_result.tsv --threads 1
[2023-03-19 00:44:36,434] [INFO] Task succeeded: fastANI
[2023-03-19 00:44:36,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:44:36,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:44:36,435] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:44:36,435] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:44:36,435] [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
--------------------------------------------------------------------------------
[2023-03-19 00:44:36,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3142/tc_result.tsv
[2023-03-19 00:44:36,436] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:44:36,436] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:44:36,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference/checkm_data
[2023-03-19 00:44:36,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:44:36,443] [INFO] Task started: CheckM
[2023-03-19 00:44:36,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3142/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3142/checkm_input OceanDNA-a3142/checkm_result
[2023-03-19 00:45:10,592] [INFO] Task succeeded: CheckM
[2023-03-19 00:45:10,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:45:10,594] [INFO] ===== Completeness check finished =====
[2023-03-19 00:45:10,595] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:45:10,595] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3142/markers.fasta)
[2023-03-19 00:45:10,596] [INFO] Task started: Blastn
[2023-03-19 00:45:10,596] [INFO] Running command: blastn -query OceanDNA-a3142/markers.fasta -db /var/lib/cwl/stg7e408aa8-ce71-4e1d-b8a2-9dbcc358200a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3142/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:45:11,015] [INFO] Task succeeded: Blastn
[2023-03-19 00:45:11,016] [INFO] Selected 15 target genomes.
[2023-03-19 00:45:11,016] [INFO] Target genome list was writen to OceanDNA-a3142/target_genomes_gtdb.txt
[2023-03-19 00:45:11,032] [INFO] Task started: fastANI
[2023-03-19 00:45:11,032] [INFO] Running command: fastANI --query /var/lib/cwl/stga955fd7f-7348-4db9-a8d6-508d6b226df6/OceanDNA-a3142.fa --refList OceanDNA-a3142/target_genomes_gtdb.txt --output OceanDNA-a3142/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:45:15,676] [INFO] Task succeeded: fastANI
[2023-03-19 00:45:15,683] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:45:15,683] [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_002726495.1	s__Poseidonia sp002726495	97.1334	500	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	97.10	97.06	0.83	0.82	3	conclusive
GCA_018662715.1	s__Poseidonia sp018662715	79.1706	207	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.82	98.76	0.75	0.74	3	-
GCA_018662825.1	s__MGIIa-L1 sp018662825	77.4258	54	609	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_000246735.1	s__MGIIa-L1 sp000246735	77.0101	59	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.40	99.32	0.97	0.89	6	-
GCA_002499705.1	s__MGIIa-L1 sp002499705	77.0028	53	609	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	76.8181	61	609	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_013330155.1	s__Poseidonia sp8339u	76.8141	73	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.08	98.16	0.89	0.82	3	-
GCA_002704515.1	s__Poseidonia sp002704515	76.7846	83	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170315.2	s__MGIIa-L1 sp002170315	76.7649	67	609	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_003602475.1	s__Poseidonia sp003602475	76.3238	85	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	95.17	95.17	0.95	0.95	2	-
GCA_016777125.1	s__MGIIa-L2 sp016777125	76.2605	53	609	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.94	99.94	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:45:15,684] [INFO] GTDB search result was written to OceanDNA-a3142/result_gtdb.tsv
[2023-03-19 00:45:15,684] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:45:15,685] [INFO] DFAST_QC result json was written to OceanDNA-a3142/dqc_result.json
[2023-03-19 00:45:15,685] [INFO] DFAST_QC completed!
[2023-03-19 00:45:15,685] [INFO] Total running time: 0h0m56s