[2023-03-16 17:50:12,190] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:50:12,191] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:50:12,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference
[2023-03-16 17:50:13,298] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:50:13,298] [INFO] Task started: Prodigal
[2023-03-16 17:50:13,299] [INFO] Running command: cat /var/lib/cwl/stg67ede3f4-17d0-4db2-9aab-caa47868615f/OceanDNA-b8949.fa | prodigal -d OceanDNA-b8949/cds.fna -a OceanDNA-b8949/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:50:20,933] [INFO] Task succeeded: Prodigal
[2023-03-16 17:50:20,933] [INFO] Task started: HMMsearch
[2023-03-16 17:50:20,933] [INFO] Running command: hmmsearch --tblout OceanDNA-b8949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference/reference_markers.hmm OceanDNA-b8949/protein.faa > /dev/null
[2023-03-16 17:50:21,118] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:50:21,119] [INFO] Found 6/6 markers.
[2023-03-16 17:50:21,131] [INFO] Query marker FASTA was written to OceanDNA-b8949/markers.fasta
[2023-03-16 17:50:21,133] [INFO] Task started: Blastn
[2023-03-16 17:50:21,133] [INFO] Running command: blastn -query OceanDNA-b8949/markers.fasta -db /var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference/reference_markers.fasta -out OceanDNA-b8949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:50:21,836] [INFO] Task succeeded: Blastn
[2023-03-16 17:50:21,838] [INFO] Selected 25 target genomes.
[2023-03-16 17:50:21,838] [INFO] Target genome list was writen to OceanDNA-b8949/target_genomes.txt
[2023-03-16 17:50:21,854] [INFO] Task started: fastANI
[2023-03-16 17:50:21,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg67ede3f4-17d0-4db2-9aab-caa47868615f/OceanDNA-b8949.fa --refList OceanDNA-b8949/target_genomes.txt --output OceanDNA-b8949/fastani_result.tsv --threads 1
[2023-03-16 17:50:35,572] [INFO] Task succeeded: fastANI
[2023-03-16 17:50:35,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:50:35,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:50:35,573] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:50:35,573] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:50:35,573] [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 17:50:35,574] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8949/tc_result.tsv
[2023-03-16 17:50:35,574] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:50:35,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:50:35,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference/checkm_data
[2023-03-16 17:50:35,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:50:35,590] [INFO] Task started: CheckM
[2023-03-16 17:50:35,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8949/checkm_input OceanDNA-b8949/checkm_result
[2023-03-16 17:51:00,352] [INFO] Task succeeded: CheckM
[2023-03-16 17:51:00,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:51:00,360] [INFO] ===== Completeness check finished =====
[2023-03-16 17:51:00,360] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:51:00,360] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8949/markers.fasta)
[2023-03-16 17:51:00,361] [INFO] Task started: Blastn
[2023-03-16 17:51:00,361] [INFO] Running command: blastn -query OceanDNA-b8949/markers.fasta -db /var/lib/cwl/stg67459a83-867f-447e-867d-bd2871a4e0de/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:51:01,478] [INFO] Task succeeded: Blastn
[2023-03-16 17:51:01,480] [INFO] Selected 19 target genomes.
[2023-03-16 17:51:01,480] [INFO] Target genome list was writen to OceanDNA-b8949/target_genomes_gtdb.txt
[2023-03-16 17:51:01,499] [INFO] Task started: fastANI
[2023-03-16 17:51:01,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg67ede3f4-17d0-4db2-9aab-caa47868615f/OceanDNA-b8949.fa --refList OceanDNA-b8949/target_genomes_gtdb.txt --output OceanDNA-b8949/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:51:06,241] [INFO] Task succeeded: fastANI
[2023-03-16 17:51:06,249] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:51:06,249] [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_004321735.1	s__MED-G14 sp004321735	92.1479	291	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.77	95.40	0.78	0.75	4	-
GCA_002703065.1	s__MED-G14 sp002703065	92.0267	233	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520835.1	s__MED-G14 sp902520835	78.0199	142	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693085.1	s__MED-G14 sp002693085	77.8505	119	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554655.1	s__MED-G14 sp902554655	77.8231	119	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.59	99.59	0.62	0.62	2	-
GCA_002702385.1	s__MED-G14 sp002702385	77.8134	116	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457715.1	s__MED-G14 sp002457715	77.6384	119	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	98.34	98.31	0.91	0.89	3	-
GCA_902574335.1	s__MED-G14 sp902574335	77.4022	55	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902515405.1	s__MED-G14 sp902515405	76.7651	86	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606555.1	s__MED-G14 sp902606555	76.5297	65	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614065.1	s__MED-G14 sp002697465	76.1243	73	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.49	95.51	0.88	0.84	14	-
GCA_902544085.1	s__MED-G14 sp902544085	75.9458	66	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.92	99.92	0.94	0.94	2	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	75.9323	53	420	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:51:06,251] [INFO] GTDB search result was written to OceanDNA-b8949/result_gtdb.tsv
[2023-03-16 17:51:06,252] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:51:06,255] [INFO] DFAST_QC result json was written to OceanDNA-b8949/dqc_result.json
[2023-03-16 17:51:06,255] [INFO] DFAST_QC completed!
[2023-03-16 17:51:06,255] [INFO] Total running time: 0h0m54s