[2023-03-18 00:35:04,578] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference
[2023-03-18 00:35:05,669] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,670] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,670] [INFO] Running command: cat /var/lib/cwl/stg053183b8-6f8f-4077-a242-2754bed01d42/OceanDNA-b8307.fa | prodigal -d OceanDNA-b8307/cds.fna -a OceanDNA-b8307/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:09,083] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:09,084] [INFO] Task started: HMMsearch
[2023-03-18 00:35:09,084] [INFO] Running command: hmmsearch --tblout OceanDNA-b8307/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference/reference_markers.hmm OceanDNA-b8307/protein.faa > /dev/null
[2023-03-18 00:35:09,247] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:09,248] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg053183b8-6f8f-4077-a242-2754bed01d42/OceanDNA-b8307.fa]
[2023-03-18 00:35:09,254] [INFO] Query marker FASTA was written to OceanDNA-b8307/markers.fasta
[2023-03-18 00:35:09,255] [INFO] Task started: Blastn
[2023-03-18 00:35:09,256] [INFO] Running command: blastn -query OceanDNA-b8307/markers.fasta -db /var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference/reference_markers.fasta -out OceanDNA-b8307/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:09,818] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:09,819] [INFO] Selected 16 target genomes.
[2023-03-18 00:35:09,819] [INFO] Target genome list was writen to OceanDNA-b8307/target_genomes.txt
[2023-03-18 00:35:09,826] [INFO] Task started: fastANI
[2023-03-18 00:35:09,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg053183b8-6f8f-4077-a242-2754bed01d42/OceanDNA-b8307.fa --refList OceanDNA-b8307/target_genomes.txt --output OceanDNA-b8307/fastani_result.tsv --threads 1
[2023-03-18 00:35:19,580] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:19,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:19,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:19,581] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:19,581] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:19,581] [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
--------------------------------------------------------------------------------
[2023-03-18 00:35:19,581] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8307/tc_result.tsv
[2023-03-18 00:35:19,581] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:19,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:19,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference/checkm_data
[2023-03-18 00:35:19,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:19,586] [INFO] Task started: CheckM
[2023-03-18 00:35:19,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8307/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8307/checkm_input OceanDNA-b8307/checkm_result
[2023-03-18 00:35:35,033] [INFO] Task succeeded: CheckM
[2023-03-18 00:35:35,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.19%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:35:35,035] [INFO] ===== Completeness check finished =====
[2023-03-18 00:35:35,035] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:35:35,035] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8307/markers.fasta)
[2023-03-18 00:35:35,035] [INFO] Task started: Blastn
[2023-03-18 00:35:35,035] [INFO] Running command: blastn -query OceanDNA-b8307/markers.fasta -db /var/lib/cwl/stgcdc77807-53e3-42c4-a937-9e0b4f0635f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8307/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:35,775] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:35,776] [INFO] Selected 15 target genomes.
[2023-03-18 00:35:35,776] [INFO] Target genome list was writen to OceanDNA-b8307/target_genomes_gtdb.txt
[2023-03-18 00:35:35,801] [INFO] Task started: fastANI
[2023-03-18 00:35:35,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg053183b8-6f8f-4077-a242-2754bed01d42/OceanDNA-b8307.fa --refList OceanDNA-b8307/target_genomes_gtdb.txt --output OceanDNA-b8307/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:35:39,354] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:39,360] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:35:39,360] [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_002729755.1	s__MED-G11 sp002729755	86.9845	153	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	95.15	95.15	0.85	0.85	2	-
GCA_902586435.1	s__MED-G11 sp902586435	86.2793	137	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.29	96.26	0.76	0.71	5	-
GCA_014239665.1	s__MED-G11 sp014239665	77.4742	60	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_902617285.1	s__MED-G11 sp902617285	77.4007	52	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.97	95.44	0.83	0.80	4	-
GCA_004214015.1	s__MED-G11 sp004214015	77.365	52	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_002457075.1	s__MED-G11 sp002457075	77.3559	63	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_004213645.1	s__MED-G11 sp004213645	77.1333	58	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.96	97.96	0.74	0.74	2	-
GCA_902577515.1	s__MED-G11 sp902577515	76.7079	55	192	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.13	99.13	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:35:39,360] [INFO] GTDB search result was written to OceanDNA-b8307/result_gtdb.tsv
[2023-03-18 00:35:39,360] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:35:39,361] [INFO] DFAST_QC result json was written to OceanDNA-b8307/dqc_result.json
[2023-03-18 00:35:39,361] [INFO] DFAST_QC completed!
[2023-03-18 00:35:39,361] [INFO] Total running time: 0h0m35s