[2023-03-16 10:20:34,600] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,600] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference
[2023-03-16 10:20:35,877] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,877] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,878] [INFO] Running command: cat /var/lib/cwl/stgfe528c19-0161-46bc-8349-e61cb09bbf29/OceanDNA-b785.fa | prodigal -d OceanDNA-b785/cds.fna -a OceanDNA-b785/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:43,748] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:43,748] [INFO] Task started: HMMsearch
[2023-03-16 10:20:43,748] [INFO] Running command: hmmsearch --tblout OceanDNA-b785/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference/reference_markers.hmm OceanDNA-b785/protein.faa > /dev/null
[2023-03-16 10:20:43,973] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:43,973] [INFO] Found 6/6 markers.
[2023-03-16 10:20:43,988] [INFO] Query marker FASTA was written to OceanDNA-b785/markers.fasta
[2023-03-16 10:20:43,988] [INFO] Task started: Blastn
[2023-03-16 10:20:43,988] [INFO] Running command: blastn -query OceanDNA-b785/markers.fasta -db /var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference/reference_markers.fasta -out OceanDNA-b785/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:44,538] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:44,541] [INFO] Selected 10 target genomes.
[2023-03-16 10:20:44,541] [INFO] Target genome list was writen to OceanDNA-b785/target_genomes.txt
[2023-03-16 10:20:44,550] [INFO] Task started: fastANI
[2023-03-16 10:20:44,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe528c19-0161-46bc-8349-e61cb09bbf29/OceanDNA-b785.fa --refList OceanDNA-b785/target_genomes.txt --output OceanDNA-b785/fastani_result.tsv --threads 1
[2023-03-16 10:20:49,861] [INFO] Task succeeded: fastANI
[2023-03-16 10:20:49,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:20:49,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:20:49,862] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:20:49,862] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:20:49,862] [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
--------------------------------------------------------------------------------
[2023-03-16 10:20:49,863] [INFO] DFAST Taxonomy check result was written to OceanDNA-b785/tc_result.tsv
[2023-03-16 10:20:49,863] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:20:49,863] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:20:49,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference/checkm_data
[2023-03-16 10:20:49,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:20:49,869] [INFO] Task started: CheckM
[2023-03-16 10:20:49,869] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b785/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b785/checkm_input OceanDNA-b785/checkm_result
[2023-03-16 10:21:14,856] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:14,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:14,858] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:14,858] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:14,858] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b785/markers.fasta)
[2023-03-16 10:21:14,858] [INFO] Task started: Blastn
[2023-03-16 10:21:14,858] [INFO] Running command: blastn -query OceanDNA-b785/markers.fasta -db /var/lib/cwl/stg72489565-77ff-46a2-bf4f-e31b52a53f77/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b785/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:15,571] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:15,572] [INFO] Selected 15 target genomes.
[2023-03-16 10:21:15,572] [INFO] Target genome list was writen to OceanDNA-b785/target_genomes_gtdb.txt
[2023-03-16 10:21:15,585] [INFO] Task started: fastANI
[2023-03-16 10:21:15,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe528c19-0161-46bc-8349-e61cb09bbf29/OceanDNA-b785.fa --refList OceanDNA-b785/target_genomes_gtdb.txt --output OceanDNA-b785/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:21,075] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:21,081] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:21:21,081] [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_002721755.1	s__MedAcidi-G1 sp002721755	99.7036	407	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002294285.1	s__MedAcidi-G1 sp002294285	82.5287	350	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.52	99.33	0.89	0.81	5	-
GCA_002299135.1	s__MedAcidi-G1 sp002299135	79.6649	204	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699555.1	s__MedAcidi-G1 sp002699555	79.3126	156	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	95.71	95.71	0.59	0.59	2	-
GCA_002716285.1	s__MedAcidi-G1 sp002716285	79.2931	204	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.29	99.25	0.75	0.74	4	-
GCA_002729765.1	s__MedAcidi-G1 sp002729765	79.1899	227	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	98.94	98.94	0.89	0.89	2	-
GCA_003214465.1	s__MedAcidi-G1 sp003214465	79.0233	236	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.48	98.96	0.92	0.84	3	-
GCA_000817085.1	s__MedAcidi-G1 sp000817085	78.6294	209	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	99.46	99.15	0.88	0.85	6	-
GCA_002713545.1	s__MedAcidi-G1 sp002713545	78.3248	173	468	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__MedAcidi-G1	95.0	98.75	98.69	0.79	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:21,082] [INFO] GTDB search result was written to OceanDNA-b785/result_gtdb.tsv
[2023-03-16 10:21:21,082] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:21,082] [INFO] DFAST_QC result json was written to OceanDNA-b785/dqc_result.json
[2023-03-16 10:21:21,083] [INFO] DFAST_QC completed!
[2023-03-16 10:21:21,083] [INFO] Total running time: 0h0m46s