[2023-03-16 16:53:43,585] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:53:43,585] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:53:43,586] [INFO] DQC Reference Directory: /var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference
[2023-03-16 16:53:44,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:53:44,674] [INFO] Task started: Prodigal
[2023-03-16 16:53:44,674] [INFO] Running command: cat /var/lib/cwl/stg91517f3a-61f3-46ca-af86-1f97fea1b6d1/OceanDNA-b5439.fa | prodigal -d OceanDNA-b5439/cds.fna -a OceanDNA-b5439/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:53:55,875] [INFO] Task succeeded: Prodigal
[2023-03-16 16:53:55,875] [INFO] Task started: HMMsearch
[2023-03-16 16:53:55,875] [INFO] Running command: hmmsearch --tblout OceanDNA-b5439/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference/reference_markers.hmm OceanDNA-b5439/protein.faa > /dev/null
[2023-03-16 16:53:56,042] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:53:56,042] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg91517f3a-61f3-46ca-af86-1f97fea1b6d1/OceanDNA-b5439.fa]
[2023-03-16 16:53:56,056] [INFO] Query marker FASTA was written to OceanDNA-b5439/markers.fasta
[2023-03-16 16:53:56,057] [INFO] Task started: Blastn
[2023-03-16 16:53:56,057] [INFO] Running command: blastn -query OceanDNA-b5439/markers.fasta -db /var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference/reference_markers.fasta -out OceanDNA-b5439/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:53:56,596] [INFO] Task succeeded: Blastn
[2023-03-16 16:53:56,597] [INFO] Selected 28 target genomes.
[2023-03-16 16:53:56,597] [INFO] Target genome list was writen to OceanDNA-b5439/target_genomes.txt
[2023-03-16 16:53:56,610] [INFO] Task started: fastANI
[2023-03-16 16:53:56,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg91517f3a-61f3-46ca-af86-1f97fea1b6d1/OceanDNA-b5439.fa --refList OceanDNA-b5439/target_genomes.txt --output OceanDNA-b5439/fastani_result.tsv --threads 1
[2023-03-16 16:54:12,882] [INFO] Task succeeded: fastANI
[2023-03-16 16:54:12,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:54:12,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:54:12,883] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:54:12,883] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:54:12,883] [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 16:54:12,883] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5439/tc_result.tsv
[2023-03-16 16:54:12,883] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:54:12,884] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:54:12,884] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference/checkm_data
[2023-03-16 16:54:12,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:54:12,892] [INFO] Task started: CheckM
[2023-03-16 16:54:12,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5439/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5439/checkm_input OceanDNA-b5439/checkm_result
[2023-03-16 16:54:57,591] [INFO] Task succeeded: CheckM
[2023-03-16 16:54:57,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.55%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:54:57,594] [INFO] ===== Completeness check finished =====
[2023-03-16 16:54:57,594] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:54:57,594] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5439/markers.fasta)
[2023-03-16 16:54:57,595] [INFO] Task started: Blastn
[2023-03-16 16:54:57,595] [INFO] Running command: blastn -query OceanDNA-b5439/markers.fasta -db /var/lib/cwl/stg98e33299-cc52-4ebc-92e7-baa3852e5ccb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5439/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:54:58,535] [INFO] Task succeeded: Blastn
[2023-03-16 16:54:58,536] [INFO] Selected 23 target genomes.
[2023-03-16 16:54:58,536] [INFO] Target genome list was writen to OceanDNA-b5439/target_genomes_gtdb.txt
[2023-03-16 16:54:58,558] [INFO] Task started: fastANI
[2023-03-16 16:54:58,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg91517f3a-61f3-46ca-af86-1f97fea1b6d1/OceanDNA-b5439.fa --refList OceanDNA-b5439/target_genomes_gtdb.txt --output OceanDNA-b5439/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:55:11,895] [INFO] Task succeeded: fastANI
[2023-03-16 16:55:11,899] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:55:11,899] [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_905182775.1	s__UBA952 sp905182775	98.1475	383	488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905182495.1	s__UBA952 sp905182495	81.7157	368	488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167775.1	s__UBA952 sp002167775	77.3923	150	488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
GCA_002480215.1	s__UBA952 sp002480215	76.9979	122	488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_002683585.1	s__UBA952 sp002683585	76.9423	80	488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:55:11,900] [INFO] GTDB search result was written to OceanDNA-b5439/result_gtdb.tsv
[2023-03-16 16:55:11,900] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:55:11,900] [INFO] DFAST_QC result json was written to OceanDNA-b5439/dqc_result.json
[2023-03-16 16:55:11,901] [INFO] DFAST_QC completed!
[2023-03-16 16:55:11,901] [INFO] Total running time: 0h1m28s