[2023-03-14 14:10:38,559] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:10:38,559] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:10:38,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference
[2023-03-14 14:10:39,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:10:39,691] [INFO] Task started: Prodigal
[2023-03-14 14:10:39,691] [INFO] Running command: cat /var/lib/cwl/stge6b3522b-6d84-4f7b-8fcf-7749deed7c2d/OceanDNA-a2996.fa | prodigal -d OceanDNA-a2996/cds.fna -a OceanDNA-a2996/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:10:49,176] [INFO] Task succeeded: Prodigal
[2023-03-14 14:10:49,176] [INFO] Task started: HMMsearch
[2023-03-14 14:10:49,176] [INFO] Running command: hmmsearch --tblout OceanDNA-a2996/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference/reference_markers.hmm OceanDNA-a2996/protein.faa > /dev/null
[2023-03-14 14:10:49,337] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:10:49,338] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge6b3522b-6d84-4f7b-8fcf-7749deed7c2d/OceanDNA-a2996.fa]
[2023-03-14 14:10:49,351] [INFO] Query marker FASTA was written to OceanDNA-a2996/markers.fasta
[2023-03-14 14:10:49,352] [INFO] Task started: Blastn
[2023-03-14 14:10:49,352] [INFO] Running command: blastn -query OceanDNA-a2996/markers.fasta -db /var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference/reference_markers.fasta -out OceanDNA-a2996/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:10:49,804] [INFO] Task succeeded: Blastn
[2023-03-14 14:10:49,805] [INFO] Selected 5 target genomes.
[2023-03-14 14:10:49,805] [INFO] Target genome list was writen to OceanDNA-a2996/target_genomes.txt
[2023-03-14 14:10:49,808] [INFO] Task started: fastANI
[2023-03-14 14:10:49,808] [INFO] Running command: fastANI --query /var/lib/cwl/stge6b3522b-6d84-4f7b-8fcf-7749deed7c2d/OceanDNA-a2996.fa --refList OceanDNA-a2996/target_genomes.txt --output OceanDNA-a2996/fastani_result.tsv --threads 1
[2023-03-14 14:10:55,493] [INFO] Task succeeded: fastANI
[2023-03-14 14:10:55,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:10:55,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:10:55,494] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:10:55,494] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:10:55,494] [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
--------------------------------------------------------------------------------
[2023-03-14 14:10:55,495] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2996/tc_result.tsv
[2023-03-14 14:10:55,495] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:10:55,495] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:10:55,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference/checkm_data
[2023-03-14 14:10:55,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:10:55,579] [INFO] Task started: CheckM
[2023-03-14 14:10:55,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2996/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2996/checkm_input OceanDNA-a2996/checkm_result
[2023-03-14 14:11:24,708] [INFO] Task succeeded: CheckM
[2023-03-14 14:11:24,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 14:11:24,710] [INFO] ===== Completeness check finished =====
[2023-03-14 14:11:24,711] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:11:24,711] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2996/markers.fasta)
[2023-03-14 14:11:24,712] [INFO] Task started: Blastn
[2023-03-14 14:11:24,712] [INFO] Running command: blastn -query OceanDNA-a2996/markers.fasta -db /var/lib/cwl/stgb0ddbb8b-4084-4b11-8c11-ce7c892439be/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2996/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:11:25,144] [INFO] Task succeeded: Blastn
[2023-03-14 14:11:25,145] [INFO] Selected 10 target genomes.
[2023-03-14 14:11:25,146] [INFO] Target genome list was writen to OceanDNA-a2996/target_genomes_gtdb.txt
[2023-03-14 14:11:25,170] [INFO] Task started: fastANI
[2023-03-14 14:11:25,170] [INFO] Running command: fastANI --query /var/lib/cwl/stge6b3522b-6d84-4f7b-8fcf-7749deed7c2d/OceanDNA-a2996.fa --refList OceanDNA-a2996/target_genomes_gtdb.txt --output OceanDNA-a2996/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:11:28,255] [INFO] Task succeeded: fastANI
[2023-03-14 14:11:28,259] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:11:28,260] [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_002495645.1	s__Poseidonia sp002495645	80.6321	305	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002689105.1	s__Poseidonia sp002689105	80.0791	265	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002725275.1	s__Poseidonia sp002725275	79.5369	215	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_016779705.1	s__Poseidonia sp016779705	78.4983	146	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694525.1	s__Poseidonia sp002694525	78.4839	178	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722695.1	s__Poseidonia sp002722695	78.2928	161	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_902625885.1	s__Poseidonia sp902625885	77.9052	133	454	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:11:28,260] [INFO] GTDB search result was written to OceanDNA-a2996/result_gtdb.tsv
[2023-03-14 14:11:28,260] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:11:28,261] [INFO] DFAST_QC result json was written to OceanDNA-a2996/dqc_result.json
[2023-03-14 14:11:28,261] [INFO] DFAST_QC completed!
[2023-03-14 14:11:28,261] [INFO] Total running time: 0h0m50s