[2023-03-16 01:21:12,517] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:21:12,520] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:21:12,520] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference
[2023-03-16 01:21:13,648] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:21:13,664] [INFO] Task started: Prodigal
[2023-03-16 01:21:13,665] [INFO] Running command: cat /var/lib/cwl/stg0b1cf574-a6ba-4053-a193-3822aedde5c4/OceanDNA-b5361.fa | prodigal -d OceanDNA-b5361/cds.fna -a OceanDNA-b5361/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:21:36,789] [INFO] Task succeeded: Prodigal
[2023-03-16 01:21:36,790] [INFO] Task started: HMMsearch
[2023-03-16 01:21:36,790] [INFO] Running command: hmmsearch --tblout OceanDNA-b5361/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference/reference_markers.hmm OceanDNA-b5361/protein.faa > /dev/null
[2023-03-16 01:21:36,994] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:21:36,995] [INFO] Found 6/6 markers.
[2023-03-16 01:21:37,056] [INFO] Query marker FASTA was written to OceanDNA-b5361/markers.fasta
[2023-03-16 01:21:37,056] [INFO] Task started: Blastn
[2023-03-16 01:21:37,056] [INFO] Running command: blastn -query OceanDNA-b5361/markers.fasta -db /var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference/reference_markers.fasta -out OceanDNA-b5361/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:21:37,593] [INFO] Task succeeded: Blastn
[2023-03-16 01:21:37,606] [INFO] Selected 26 target genomes.
[2023-03-16 01:21:37,607] [INFO] Target genome list was writen to OceanDNA-b5361/target_genomes.txt
[2023-03-16 01:21:37,678] [INFO] Task started: fastANI
[2023-03-16 01:21:37,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b1cf574-a6ba-4053-a193-3822aedde5c4/OceanDNA-b5361.fa --refList OceanDNA-b5361/target_genomes.txt --output OceanDNA-b5361/fastani_result.tsv --threads 1
[2023-03-16 01:21:52,289] [INFO] Task succeeded: fastANI
[2023-03-16 01:21:52,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:21:52,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:21:52,293] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:21:52,293] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 01:21:52,293] [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
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.0378	59	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 01:21:52,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5361/tc_result.tsv
[2023-03-16 01:21:52,323] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:21:52,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:21:52,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference/checkm_data
[2023-03-16 01:21:52,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:21:52,331] [INFO] Task started: CheckM
[2023-03-16 01:21:52,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5361/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5361/checkm_input OceanDNA-b5361/checkm_result
[2023-03-16 01:22:52,110] [INFO] Task succeeded: CheckM
[2023-03-16 01:22:52,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:22:52,394] [INFO] ===== Completeness check finished =====
[2023-03-16 01:22:52,394] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:22:52,394] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5361/markers.fasta)
[2023-03-16 01:22:52,395] [INFO] Task started: Blastn
[2023-03-16 01:22:52,395] [INFO] Running command: blastn -query OceanDNA-b5361/markers.fasta -db /var/lib/cwl/stg0fccbcff-869c-45f9-9b91-b9c0f00c1566/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5361/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:22:53,166] [INFO] Task succeeded: Blastn
[2023-03-16 01:22:53,175] [INFO] Selected 25 target genomes.
[2023-03-16 01:22:53,175] [INFO] Target genome list was writen to OceanDNA-b5361/target_genomes_gtdb.txt
[2023-03-16 01:22:53,536] [INFO] Task started: fastANI
[2023-03-16 01:22:53,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b1cf574-a6ba-4053-a193-3822aedde5c4/OceanDNA-b5361.fa --refList OceanDNA-b5361/target_genomes_gtdb.txt --output OceanDNA-b5361/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:23:06,285] [INFO] Task succeeded: fastANI
[2023-03-16 01:23:06,292] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:23:06,292] [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_015665275.1	s__UBA4466 sp015665275	78.053	178	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149635.1	s__UBA4466 sp003149635	77.3936	182	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	76.7576	82	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373595.1	s__UBA4466 sp013373595	76.5971	100	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215515.1	s__UBA4466 sp013215515	76.4808	75	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	76.4696	91	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_002427735.1	s__UBA4466 sp002427735	76.3632	92	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983675.1	s__Fluviicola sp017983675	76.3063	57	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	99.86	99.86	0.97	0.97	2	-
GCA_002733985.1	s__UBA4466 sp002733985	76.296	95	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
GCF_000194605.1	s__Fluviicola taffensis	76.0649	58	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:23:06,298] [INFO] GTDB search result was written to OceanDNA-b5361/result_gtdb.tsv
[2023-03-16 01:23:06,307] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:23:06,315] [INFO] DFAST_QC result json was written to OceanDNA-b5361/dqc_result.json
[2023-03-16 01:23:06,315] [INFO] DFAST_QC completed!
[2023-03-16 01:23:06,315] [INFO] Total running time: 0h1m54s