[2023-03-17 10:19:15,247] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:19:15,248] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:19:15,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference
[2023-03-17 10:19:16,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:19:16,989] [INFO] Task started: Prodigal
[2023-03-17 10:19:16,989] [INFO] Running command: cat /var/lib/cwl/stg64c882f5-e7ab-49e5-917d-fca7d5d0d1ae/OceanDNA-a3455.fa | prodigal -d OceanDNA-a3455/cds.fna -a OceanDNA-a3455/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:19:23,939] [INFO] Task succeeded: Prodigal
[2023-03-17 10:19:23,940] [INFO] Task started: HMMsearch
[2023-03-17 10:19:23,940] [INFO] Running command: hmmsearch --tblout OceanDNA-a3455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference/reference_markers.hmm OceanDNA-a3455/protein.faa > /dev/null
[2023-03-17 10:19:24,091] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:19:24,091] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg64c882f5-e7ab-49e5-917d-fca7d5d0d1ae/OceanDNA-a3455.fa]
[2023-03-17 10:19:24,108] [INFO] Query marker FASTA was written to OceanDNA-a3455/markers.fasta
[2023-03-17 10:19:24,108] [INFO] Task started: Blastn
[2023-03-17 10:19:24,108] [INFO] Running command: blastn -query OceanDNA-a3455/markers.fasta -db /var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference/reference_markers.fasta -out OceanDNA-a3455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:24,536] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:24,540] [INFO] Selected 4 target genomes.
[2023-03-17 10:19:24,541] [INFO] Target genome list was writen to OceanDNA-a3455/target_genomes.txt
[2023-03-17 10:19:24,543] [INFO] Task started: fastANI
[2023-03-17 10:19:24,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg64c882f5-e7ab-49e5-917d-fca7d5d0d1ae/OceanDNA-a3455.fa --refList OceanDNA-a3455/target_genomes.txt --output OceanDNA-a3455/fastani_result.tsv --threads 1
[2023-03-17 10:19:26,237] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:26,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:19:26,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:19:26,237] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:19:26,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:19:26,238] [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 10:19:26,239] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3455/tc_result.tsv
[2023-03-17 10:19:26,240] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:19:26,240] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:19:26,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference/checkm_data
[2023-03-17 10:19:26,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:19:26,247] [INFO] Task started: CheckM
[2023-03-17 10:19:26,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3455/checkm_input OceanDNA-a3455/checkm_result
[2023-03-17 10:19:49,267] [INFO] Task succeeded: CheckM
[2023-03-17 10:19:49,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:19:49,292] [INFO] ===== Completeness check finished =====
[2023-03-17 10:19:49,292] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:19:49,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3455/markers.fasta)
[2023-03-17 10:19:49,294] [INFO] Task started: Blastn
[2023-03-17 10:19:49,294] [INFO] Running command: blastn -query OceanDNA-a3455/markers.fasta -db /var/lib/cwl/stg34016d7a-9219-42bf-a94c-b71c11d6a37e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:19:49,724] [INFO] Task succeeded: Blastn
[2023-03-17 10:19:49,727] [INFO] Selected 7 target genomes.
[2023-03-17 10:19:49,727] [INFO] Target genome list was writen to OceanDNA-a3455/target_genomes_gtdb.txt
[2023-03-17 10:19:49,846] [INFO] Task started: fastANI
[2023-03-17 10:19:49,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg64c882f5-e7ab-49e5-917d-fca7d5d0d1ae/OceanDNA-a3455.fa --refList OceanDNA-a3455/target_genomes_gtdb.txt --output OceanDNA-a3455/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:19:51,885] [INFO] Task succeeded: fastANI
[2023-03-17 10:19:51,890] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:19:51,891] [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_902560445.1	s__MGIIb-O1 sp902560445	94.9366	280	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002497025.1	s__MGIIb-O1 sp002497025	93.4593	350	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.97	96.74	0.84	0.76	4	-
GCA_002457555.1	s__MGIIb-O1 sp002457555	90.4466	325	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.79	99.79	0.86	0.86	2	-
GCA_002502175.1	s__MGIIb-O1 sp002502175	84.4851	319	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.79	95.28	0.87	0.80	11	-
GCA_002496905.1	s__MGIIb-O1 sp002496905	84.1359	286	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.08	98.67	0.77	0.73	3	-
GCA_002685415.1	s__MGIIb-O1 sp002685415	82.5164	262	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	96.63	96.41	0.81	0.77	3	-
GCA_002708385.1	s__MGIIb-O1 sp002708385	80.495	172	411	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:19:51,893] [INFO] GTDB search result was written to OceanDNA-a3455/result_gtdb.tsv
[2023-03-17 10:19:51,894] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:19:51,897] [INFO] DFAST_QC result json was written to OceanDNA-a3455/dqc_result.json
[2023-03-17 10:19:51,897] [INFO] DFAST_QC completed!
[2023-03-17 10:19:51,897] [INFO] Total running time: 0h0m37s