[2023-06-29 22:30:18,035] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:30:18,037] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:30:18,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference
[2023-06-29 22:30:19,473] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:30:19,473] [INFO] Task started: Prodigal
[2023-06-29 22:30:19,474] [INFO] Running command: gunzip -c /var/lib/cwl/stg160af41b-7086-435d-bce4-4dfd243960bc/GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna.gz | prodigal -d GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/cds.fna -a GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:30:22,000] [INFO] Task succeeded: Prodigal
[2023-06-29 22:30:22,000] [INFO] Task started: HMMsearch
[2023-06-29 22:30:22,001] [INFO] Running command: hmmsearch --tblout GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference/reference_markers.hmm GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:30:22,213] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:30:22,214] [INFO] Found 6/6 markers.
[2023-06-29 22:30:22,228] [INFO] Query marker FASTA was written to GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/markers.fasta
[2023-06-29 22:30:22,228] [INFO] Task started: Blastn
[2023-06-29 22:30:22,228] [INFO] Running command: blastn -query GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/markers.fasta -db /var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference/reference_markers.fasta -out GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:22,949] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:22,958] [INFO] Selected 15 target genomes.
[2023-06-29 22:30:22,958] [INFO] Target genome list was writen to GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/target_genomes.txt
[2023-06-29 22:30:22,961] [INFO] Task started: fastANI
[2023-06-29 22:30:22,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg160af41b-7086-435d-bce4-4dfd243960bc/GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna.gz --refList GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/target_genomes.txt --output GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:30:28,369] [INFO] Task succeeded: fastANI
[2023-06-29 22:30:28,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:30:28,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:30:28,372] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:30:28,372] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:30:28,372] [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
--------------------------------------------------------------------------------
[2023-06-29 22:30:28,374] [INFO] DFAST Taxonomy check result was written to GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/tc_result.tsv
[2023-06-29 22:30:28,374] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:30:28,375] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:30:28,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference/checkm_data
[2023-06-29 22:30:28,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:30:28,394] [INFO] Task started: CheckM
[2023-06-29 22:30:28,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/checkm_input GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/checkm_result
[2023-06-29 22:30:44,862] [INFO] Task succeeded: CheckM
[2023-06-29 22:30:44,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 22:30:44,885] [INFO] ===== Completeness check finished =====
[2023-06-29 22:30:44,886] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:30:44,886] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/markers.fasta)
[2023-06-29 22:30:44,886] [INFO] Task started: Blastn
[2023-06-29 22:30:44,886] [INFO] Running command: blastn -query GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/markers.fasta -db /var/lib/cwl/stg363af107-2430-4816-b15a-35aff06088dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:45,745] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:45,750] [INFO] Selected 12 target genomes.
[2023-06-29 22:30:45,750] [INFO] Target genome list was writen to GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:30:45,756] [INFO] Task started: fastANI
[2023-06-29 22:30:45,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg160af41b-7086-435d-bce4-4dfd243960bc/GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna.gz --refList GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/target_genomes_gtdb.txt --output GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:30:47,716] [INFO] Task succeeded: fastANI
[2023-06-29 22:30:47,730] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:30:47,730] [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_903862375.1	s__UBA8515 sp903862375	100.0	247	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	99.87	99.83	0.87	0.78	4	conclusive
GCA_903825265.1	s__UBA8515 sp903825265	78.6141	59	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929735.1	s__UBA8515 sp903929735	78.3931	91	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	99.79	99.79	0.96	0.96	2	-
GCA_000990325.1	s__UBA8515 sp000990325	78.2629	79	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	99.97	99.95	0.94	0.88	7	-
GCA_903821415.1	s__UBA8515 sp903821415	78.2465	64	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000991405.1	s__UBA8515 sp000991405	77.9308	76	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	99.97	99.92	0.99	0.96	16	-
GCA_903834665.1	s__UBA8515 sp903834665	77.7983	53	250	d__Bacteria;p__Patescibacteria;c__Paceibacteria;o__UBA9983_A;f__UBA9973;g__UBA8515	95.0	99.88	99.88	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-29 22:30:47,734] [INFO] GTDB search result was written to GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/result_gtdb.tsv
[2023-06-29 22:30:47,735] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:30:47,739] [INFO] DFAST_QC result json was written to GCA_903862375.1_freshwater_MAG_---_AM-2014-D8_bin-0749_genomic.fna/dqc_result.json
[2023-06-29 22:30:47,740] [INFO] DFAST_QC completed!
[2023-06-29 22:30:47,741] [INFO] Total running time: 0h0m30s