[2023-03-15 10:49:28,630] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,630] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,630] [INFO] DQC Reference Directory: /var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference
[2023-03-15 10:49:29,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,737] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,737] [INFO] Running command: cat /var/lib/cwl/stg23b10e57-8e1b-4f57-9d93-695333a68de8/OceanDNA-b9653.fa | prodigal -d OceanDNA-b9653/cds.fna -a OceanDNA-b9653/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:55,185] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:55,185] [INFO] Task started: HMMsearch
[2023-03-15 10:49:55,185] [INFO] Running command: hmmsearch --tblout OceanDNA-b9653/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference/reference_markers.hmm OceanDNA-b9653/protein.faa > /dev/null
[2023-03-15 10:49:55,411] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:55,411] [INFO] Found 6/6 markers.
[2023-03-15 10:49:55,439] [INFO] Query marker FASTA was written to OceanDNA-b9653/markers.fasta
[2023-03-15 10:49:55,441] [INFO] Task started: Blastn
[2023-03-15 10:49:55,441] [INFO] Running command: blastn -query OceanDNA-b9653/markers.fasta -db /var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference/reference_markers.fasta -out OceanDNA-b9653/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:56,043] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:56,044] [INFO] Selected 17 target genomes.
[2023-03-15 10:49:56,045] [INFO] Target genome list was writen to OceanDNA-b9653/target_genomes.txt
[2023-03-15 10:49:56,056] [INFO] Task started: fastANI
[2023-03-15 10:49:56,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b10e57-8e1b-4f57-9d93-695333a68de8/OceanDNA-b9653.fa --refList OceanDNA-b9653/target_genomes.txt --output OceanDNA-b9653/fastani_result.tsv --threads 1
[2023-03-15 10:50:11,380] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:11,380] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:50:11,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:50:11,391] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:50:11,391] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:50:11,391] [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
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	88.1425	1048	1339	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	88.1331	1039	1339	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	81.5388	812	1339	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	81.2319	812	1339	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	81.2257	826	1339	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	80.8557	768	1339	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.7913	806	1339	95	below_threshold
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	80.6377	725	1339	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	80.2741	707	1339	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	80.1417	726	1339	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	80.107	717	1339	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.9849	228	1339	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.739	228	1339	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	75.9804	98	1339	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	75.8438	80	1339	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.7314	87	1339	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.2671	85	1339	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:50:11,392] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9653/tc_result.tsv
[2023-03-15 10:50:11,392] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:50:11,392] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:50:11,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference/checkm_data
[2023-03-15 10:50:11,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:50:11,401] [INFO] Task started: CheckM
[2023-03-15 10:50:11,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9653/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9653/checkm_input OceanDNA-b9653/checkm_result
[2023-03-15 10:51:15,284] [INFO] Task succeeded: CheckM
[2023-03-15 10:51:15,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:51:15,288] [INFO] ===== Completeness check finished =====
[2023-03-15 10:51:15,288] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:51:15,288] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9653/markers.fasta)
[2023-03-15 10:51:15,289] [INFO] Task started: Blastn
[2023-03-15 10:51:15,289] [INFO] Running command: blastn -query OceanDNA-b9653/markers.fasta -db /var/lib/cwl/stga550e3e0-9244-4780-b4df-9a849c16ffdf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9653/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:51:16,120] [INFO] Task succeeded: Blastn
[2023-03-15 10:51:16,121] [INFO] Selected 13 target genomes.
[2023-03-15 10:51:16,121] [INFO] Target genome list was writen to OceanDNA-b9653/target_genomes_gtdb.txt
[2023-03-15 10:51:16,162] [INFO] Task started: fastANI
[2023-03-15 10:51:16,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg23b10e57-8e1b-4f57-9d93-695333a68de8/OceanDNA-b9653.fa --refList OceanDNA-b9653/target_genomes_gtdb.txt --output OceanDNA-b9653/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:51:27,254] [INFO] Task succeeded: fastANI
[2023-03-15 10:51:27,262] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:51:27,262] [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
GCF_001913155.1	s__Maribacter hydrothermalis	88.1336	1049	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004364175.1	s__Maribacter caenipelagi	81.5388	812	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	81.2289	812	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	81.2223	827	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075045.1	s__Maribacter litoralis	80.8717	766	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.43	97.43	0.90	0.90	2	-
GCF_900112245.1	s__Maribacter stanieri	80.7912	806	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900155985.1	s__Maribacter ulvicola	80.6295	726	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.5156	762	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900167935.1	s__Maribacter arcticus	80.2665	708	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	80.134	727	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	80.1097	717	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_003970695.1	s__Maribacter sp002742365	76.7508	188	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.61	96.61	0.86	0.86	2	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.739	228	1339	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:51:27,263] [INFO] GTDB search result was written to OceanDNA-b9653/result_gtdb.tsv
[2023-03-15 10:51:27,263] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:51:27,265] [INFO] DFAST_QC result json was written to OceanDNA-b9653/dqc_result.json
[2023-03-15 10:51:27,265] [INFO] DFAST_QC completed!
[2023-03-15 10:51:27,265] [INFO] Total running time: 0h1m59s