[2023-03-17 09:05:02,549] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,549] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference
[2023-03-17 09:05:03,729] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,729] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,729] [INFO] Running command: cat /var/lib/cwl/stg8e57cb59-aedd-4be8-bf50-87e1fbbc02aa/OceanDNA-b46641.fa | prodigal -d OceanDNA-b46641/cds.fna -a OceanDNA-b46641/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:33,524] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:33,525] [INFO] Task started: HMMsearch
[2023-03-17 09:05:33,525] [INFO] Running command: hmmsearch --tblout OceanDNA-b46641/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference/reference_markers.hmm OceanDNA-b46641/protein.faa > /dev/null
[2023-03-17 09:05:33,733] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:33,734] [INFO] Found 6/6 markers.
[2023-03-17 09:05:33,754] [INFO] Query marker FASTA was written to OceanDNA-b46641/markers.fasta
[2023-03-17 09:05:33,755] [INFO] Task started: Blastn
[2023-03-17 09:05:33,755] [INFO] Running command: blastn -query OceanDNA-b46641/markers.fasta -db /var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference/reference_markers.fasta -out OceanDNA-b46641/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:34,295] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:34,296] [INFO] Selected 24 target genomes.
[2023-03-17 09:05:34,297] [INFO] Target genome list was writen to OceanDNA-b46641/target_genomes.txt
[2023-03-17 09:05:34,385] [INFO] Task started: fastANI
[2023-03-17 09:05:34,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e57cb59-aedd-4be8-bf50-87e1fbbc02aa/OceanDNA-b46641.fa --refList OceanDNA-b46641/target_genomes.txt --output OceanDNA-b46641/fastani_result.tsv --threads 1
[2023-03-17 09:05:52,959] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:52,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:52,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:52,959] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:52,959] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:52,959] [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
--------------------------------------------------------------------------------
[2023-03-17 09:05:52,960] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46641/tc_result.tsv
[2023-03-17 09:05:52,960] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:52,960] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:52,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference/checkm_data
[2023-03-17 09:05:52,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:53,039] [INFO] Task started: CheckM
[2023-03-17 09:05:53,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46641/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46641/checkm_input OceanDNA-b46641/checkm_result
[2023-03-17 09:07:03,107] [INFO] Task succeeded: CheckM
[2023-03-17 09:07:03,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.85%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-17 09:07:03,110] [INFO] ===== Completeness check finished =====
[2023-03-17 09:07:03,110] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:07:03,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46641/markers.fasta)
[2023-03-17 09:07:03,112] [INFO] Task started: Blastn
[2023-03-17 09:07:03,112] [INFO] Running command: blastn -query OceanDNA-b46641/markers.fasta -db /var/lib/cwl/stgb25aee62-22e1-48ce-926f-8bf12636e7e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46641/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:07:03,937] [INFO] Task succeeded: Blastn
[2023-03-17 09:07:03,938] [INFO] Selected 15 target genomes.
[2023-03-17 09:07:03,938] [INFO] Target genome list was writen to OceanDNA-b46641/target_genomes_gtdb.txt
[2023-03-17 09:07:04,081] [INFO] Task started: fastANI
[2023-03-17 09:07:04,081] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e57cb59-aedd-4be8-bf50-87e1fbbc02aa/OceanDNA-b46641.fa --refList OceanDNA-b46641/target_genomes_gtdb.txt --output OceanDNA-b46641/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:07:12,852] [INFO] Task succeeded: fastANI
[2023-03-17 09:07:12,858] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:07:12,858] [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_002721895.1	s__UBA6614 sp002721895	99.8279	796	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	97.45	95.11	0.88	0.86	3	conclusive
GCA_002718935.1	s__UBA1100 sp002718935	81.3549	125	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724615.1	s__UBA6614 sp002724615	78.9017	114	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523245.1	s__UBA1100 sp011523245	78.881	91	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382585.1	s__JACNJL01 sp014382585	77.8509	173	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239365.1	s__JACNJL01 sp014239365	77.1875	139	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	76.4853	55	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695465.1	s__SYLI01 sp009695465	76.4135	77	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__SYLI01	95.0	99.82	99.82	0.91	0.91	2	-
GCA_005809105.1	s__SYLI01 sp005809105	75.9367	65	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__SYLI01	95.0	99.90	99.86	0.97	0.96	4	-
GCA_014193395.1	s__BJHT01 sp014193395	75.2483	55	872	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__BJHT01;g__BJHT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:07:12,859] [INFO] GTDB search result was written to OceanDNA-b46641/result_gtdb.tsv
[2023-03-17 09:07:12,859] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:07:12,859] [INFO] DFAST_QC result json was written to OceanDNA-b46641/dqc_result.json
[2023-03-17 09:07:12,860] [INFO] DFAST_QC completed!
[2023-03-17 09:07:12,860] [INFO] Total running time: 0h2m10s