[2023-03-15 13:45:07,857] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,857] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,857] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference
[2023-03-15 13:45:09,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stgbe232598-0f60-4d38-a1e2-69d5eeee7aaf/OceanDNA-b15043.fa | prodigal -d OceanDNA-b15043/cds.fna -a OceanDNA-b15043/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:15,373] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:15,373] [INFO] Task started: HMMsearch
[2023-03-15 13:45:15,373] [INFO] Running command: hmmsearch --tblout OceanDNA-b15043/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference/reference_markers.hmm OceanDNA-b15043/protein.faa > /dev/null
[2023-03-15 13:45:15,519] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:15,519] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbe232598-0f60-4d38-a1e2-69d5eeee7aaf/OceanDNA-b15043.fa]
[2023-03-15 13:45:15,529] [INFO] Query marker FASTA was written to OceanDNA-b15043/markers.fasta
[2023-03-15 13:45:15,529] [INFO] Task started: Blastn
[2023-03-15 13:45:15,529] [INFO] Running command: blastn -query OceanDNA-b15043/markers.fasta -db /var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference/reference_markers.fasta -out OceanDNA-b15043/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:16,015] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:16,016] [INFO] Selected 11 target genomes.
[2023-03-15 13:45:16,016] [INFO] Target genome list was writen to OceanDNA-b15043/target_genomes.txt
[2023-03-15 13:45:16,024] [INFO] Task started: fastANI
[2023-03-15 13:45:16,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe232598-0f60-4d38-a1e2-69d5eeee7aaf/OceanDNA-b15043.fa --refList OceanDNA-b15043/target_genomes.txt --output OceanDNA-b15043/fastani_result.tsv --threads 1
[2023-03-15 13:45:20,817] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:20,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:20,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:20,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:45:20,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:45:20,818] [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 13:45:20,818] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15043/tc_result.tsv
[2023-03-15 13:45:20,818] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:20,818] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:20,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference/checkm_data
[2023-03-15 13:45:20,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:20,839] [INFO] Task started: CheckM
[2023-03-15 13:45:20,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15043/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15043/checkm_input OceanDNA-b15043/checkm_result
[2023-03-15 13:45:41,521] [INFO] Task succeeded: CheckM
[2023-03-15 13:45:41,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:45:41,523] [INFO] ===== Completeness check finished =====
[2023-03-15 13:45:41,523] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:45:41,523] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15043/markers.fasta)
[2023-03-15 13:45:41,525] [INFO] Task started: Blastn
[2023-03-15 13:45:41,525] [INFO] Running command: blastn -query OceanDNA-b15043/markers.fasta -db /var/lib/cwl/stgc8d6b109-682d-4e27-a7d1-0f4202606478/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15043/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:42,151] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:42,152] [INFO] Selected 14 target genomes.
[2023-03-15 13:45:42,152] [INFO] Target genome list was writen to OceanDNA-b15043/target_genomes_gtdb.txt
[2023-03-15 13:45:42,167] [INFO] Task started: fastANI
[2023-03-15 13:45:42,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe232598-0f60-4d38-a1e2-69d5eeee7aaf/OceanDNA-b15043.fa --refList OceanDNA-b15043/target_genomes_gtdb.txt --output OceanDNA-b15043/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:45:46,484] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:46,490] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:45:46,490] [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_002711965.1	s__TMED-70 sp002711965	98.9594	342	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	98.97	98.97	0.82	0.82	2	conclusive
GCA_002710135.1	s__TMED-70 sp002710135	83.2068	250	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699165.1	s__TMED-70 sp002699165	81.7764	317	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.00	98.33	0.87	0.75	4	-
GCA_002719425.1	s__TMED-70 sp002719425	78.9089	186	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002703265.1	s__TMED-70 sp002703265	78.5252	221	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	97.70	96.59	0.89	0.70	8	-
GCA_002171675.1	s__TMED-70 sp002171675	77.8264	139	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.24	99.20	0.89	0.87	3	-
GCA_009937255.1	s__TMED-70 sp009937255	77.676	149	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	96.35	96.35	0.92	0.92	2	-
GCA_002721875.1	s__TMED-70 sp002721875	77.2692	131	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718455.1	s__GCA-2718455 sp002718455	76.7169	66	404	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2718455	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:45:46,491] [INFO] GTDB search result was written to OceanDNA-b15043/result_gtdb.tsv
[2023-03-15 13:45:46,491] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:45:46,492] [INFO] DFAST_QC result json was written to OceanDNA-b15043/dqc_result.json
[2023-03-15 13:45:46,492] [INFO] DFAST_QC completed!
[2023-03-15 13:45:46,492] [INFO] Total running time: 0h0m39s