[2023-03-19 03:50:07,840] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,840] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference
[2023-03-19 03:50:09,609] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,609] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,609] [INFO] Running command: cat /var/lib/cwl/stg36b74173-4d98-489c-9d85-159c3d2e24f7/OceanDNA-b9344.fa | prodigal -d OceanDNA-b9344/cds.fna -a OceanDNA-b9344/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:20,142] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:20,143] [INFO] Task started: HMMsearch
[2023-03-19 03:50:20,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b9344/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference/reference_markers.hmm OceanDNA-b9344/protein.faa > /dev/null
[2023-03-19 03:50:20,380] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:20,380] [INFO] Found 6/6 markers.
[2023-03-19 03:50:20,394] [INFO] Query marker FASTA was written to OceanDNA-b9344/markers.fasta
[2023-03-19 03:50:20,395] [INFO] Task started: Blastn
[2023-03-19 03:50:20,395] [INFO] Running command: blastn -query OceanDNA-b9344/markers.fasta -db /var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference/reference_markers.fasta -out OceanDNA-b9344/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:20,959] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:20,959] [INFO] Selected 32 target genomes.
[2023-03-19 03:50:20,960] [INFO] Target genome list was writen to OceanDNA-b9344/target_genomes.txt
[2023-03-19 03:50:20,974] [INFO] Task started: fastANI
[2023-03-19 03:50:20,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg36b74173-4d98-489c-9d85-159c3d2e24f7/OceanDNA-b9344.fa --refList OceanDNA-b9344/target_genomes.txt --output OceanDNA-b9344/fastani_result.tsv --threads 1
[2023-03-19 03:50:39,462] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:39,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:39,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:39,462] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:39,462] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:39,462] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:39,463] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9344/tc_result.tsv
[2023-03-19 03:50:39,463] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:39,463] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:39,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference/checkm_data
[2023-03-19 03:50:39,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:39,469] [INFO] Task started: CheckM
[2023-03-19 03:50:39,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9344/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9344/checkm_input OceanDNA-b9344/checkm_result
[2023-03-19 03:51:10,127] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:10,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:10,129] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:10,129] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:10,129] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9344/markers.fasta)
[2023-03-19 03:51:10,129] [INFO] Task started: Blastn
[2023-03-19 03:51:10,130] [INFO] Running command: blastn -query OceanDNA-b9344/markers.fasta -db /var/lib/cwl/stgc5803679-b414-42a8-96dc-70d94d0f5439/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9344/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:10,905] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:10,906] [INFO] Selected 17 target genomes.
[2023-03-19 03:51:10,906] [INFO] Target genome list was writen to OceanDNA-b9344/target_genomes_gtdb.txt
[2023-03-19 03:51:10,925] [INFO] Task started: fastANI
[2023-03-19 03:51:10,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg36b74173-4d98-489c-9d85-159c3d2e24f7/OceanDNA-b9344.fa --refList OceanDNA-b9344/target_genomes_gtdb.txt --output OceanDNA-b9344/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:51:17,482] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:17,490] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:51:17,490] [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_905480425.1	s__MS024-2A sp905480425	99.6428	510	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	conclusive
GCA_905182305.1	s__MS024-2A sp905182305	93.8541	474	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009886625.1	s__MS024-2A sp009886625	78.0573	208	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000173095.1	s__MS024-2A sp000173095	78.0459	223	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.61	99.48	0.88	0.84	16	-
GCA_905181895.1	s__MS024-2A sp905181895	77.827	140	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546725.1	s__MS024-2A sp902546725	77.5932	69	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512755.1	s__MS024-2A sp902512755	77.1616	83	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606525.1	s__MS024-2A sp902606525	77.1179	77	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182575.1	s__UBA8316 sp905182575	77.0742	73	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	95.72	95.72	0.87	0.87	2	-
GCA_902517245.1	s__MS024-2A sp902517245	77.0626	108	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017851655.1	s__MS024-2A sp017851655	76.6776	128	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.55	99.53	0.87	0.86	3	-
GCA_017852075.1	s__MS024-2A sp017852075	76.6494	99	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_017858055.1	s__MS024-2A sp002384715	76.5472	106	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.54	99.54	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:51:17,490] [INFO] GTDB search result was written to OceanDNA-b9344/result_gtdb.tsv
[2023-03-19 03:51:17,490] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:51:17,491] [INFO] DFAST_QC result json was written to OceanDNA-b9344/dqc_result.json
[2023-03-19 03:51:17,491] [INFO] DFAST_QC completed!
[2023-03-19 03:51:17,491] [INFO] Total running time: 0h1m10s