[2023-03-17 23:00:49,596] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:00:49,596] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:00:49,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference
[2023-03-17 23:00:52,223] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:00:52,224] [INFO] Task started: Prodigal
[2023-03-17 23:00:52,224] [INFO] Running command: cat /var/lib/cwl/stgfdd6f219-6fdc-42a4-aef9-be9814293ace/OceanDNA-a1838.fa | prodigal -d OceanDNA-a1838/cds.fna -a OceanDNA-a1838/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:00:58,758] [INFO] Task succeeded: Prodigal
[2023-03-17 23:00:58,758] [INFO] Task started: HMMsearch
[2023-03-17 23:00:58,758] [INFO] Running command: hmmsearch --tblout OceanDNA-a1838/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference/reference_markers.hmm OceanDNA-a1838/protein.faa > /dev/null
[2023-03-17 23:00:58,981] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:00:58,982] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfdd6f219-6fdc-42a4-aef9-be9814293ace/OceanDNA-a1838.fa]
[2023-03-17 23:00:58,993] [INFO] Query marker FASTA was written to OceanDNA-a1838/markers.fasta
[2023-03-17 23:00:58,995] [INFO] Task started: Blastn
[2023-03-17 23:00:58,995] [INFO] Running command: blastn -query OceanDNA-a1838/markers.fasta -db /var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference/reference_markers.fasta -out OceanDNA-a1838/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:01:02,440] [INFO] Task succeeded: Blastn
[2023-03-17 23:01:02,441] [INFO] Selected 5 target genomes.
[2023-03-17 23:01:02,441] [INFO] Target genome list was writen to OceanDNA-a1838/target_genomes.txt
[2023-03-17 23:01:02,445] [INFO] Task started: fastANI
[2023-03-17 23:01:02,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd6f219-6fdc-42a4-aef9-be9814293ace/OceanDNA-a1838.fa --refList OceanDNA-a1838/target_genomes.txt --output OceanDNA-a1838/fastani_result.tsv --threads 1
[2023-03-17 23:01:04,954] [INFO] Task succeeded: fastANI
[2023-03-17 23:01:04,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:01:04,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:01:04,955] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:01:04,955] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:01:04,955] [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
--------------------------------------------------------------------------------
[2023-03-17 23:01:04,955] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1838/tc_result.tsv
[2023-03-17 23:01:04,955] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:01:04,955] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:01:04,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference/checkm_data
[2023-03-17 23:01:04,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:01:04,969] [INFO] Task started: CheckM
[2023-03-17 23:01:04,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1838/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1838/checkm_input OceanDNA-a1838/checkm_result
[2023-03-17 23:01:29,366] [INFO] Task succeeded: CheckM
[2023-03-17 23:01:29,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.19%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:01:29,368] [INFO] ===== Completeness check finished =====
[2023-03-17 23:01:29,368] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:01:29,368] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1838/markers.fasta)
[2023-03-17 23:01:29,369] [INFO] Task started: Blastn
[2023-03-17 23:01:29,369] [INFO] Running command: blastn -query OceanDNA-a1838/markers.fasta -db /var/lib/cwl/stgf946b7f7-ba62-454d-bd92-3458a43a4067/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1838/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:01:29,940] [INFO] Task succeeded: Blastn
[2023-03-17 23:01:29,941] [INFO] Selected 10 target genomes.
[2023-03-17 23:01:29,941] [INFO] Target genome list was writen to OceanDNA-a1838/target_genomes_gtdb.txt
[2023-03-17 23:01:29,952] [INFO] Task started: fastANI
[2023-03-17 23:01:29,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdd6f219-6fdc-42a4-aef9-be9814293ace/OceanDNA-a1838.fa --refList OceanDNA-a1838/target_genomes_gtdb.txt --output OceanDNA-a1838/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:01:32,683] [INFO] Task succeeded: fastANI
[2023-03-17 23:01:32,687] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:01:32,687] [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_002692465.1	s__MGIIa-I sp002692465	98.5261	326	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002720275.1	s__MGIIa-I sp002720275	92.0042	363	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	98.73	98.73	0.82	0.82	2	-
GCA_002498205.1	s__MGIIa-I sp002498205	83.4336	264	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696315.1	s__MGIIa-I sp002696315	82.0409	322	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.61	99.61	0.93	0.93	2	-
GCA_002699515.1	s__MGIIa-I sp002699515	79.9807	223	408	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:01:32,687] [INFO] GTDB search result was written to OceanDNA-a1838/result_gtdb.tsv
[2023-03-17 23:01:32,688] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:01:32,690] [INFO] DFAST_QC result json was written to OceanDNA-a1838/dqc_result.json
[2023-03-17 23:01:32,690] [INFO] DFAST_QC completed!
[2023-03-17 23:01:32,690] [INFO] Total running time: 0h0m43s