[2023-06-30 04:11:38,140] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:11:38,142] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:11:38,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference
[2023-06-30 04:11:39,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:11:39,530] [INFO] Task started: Prodigal
[2023-06-30 04:11:39,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg5feaa4cf-ca05-4862-9343-ddc867f37303/GCA_016708875.1_ASM1670887v1_genomic.fna.gz | prodigal -d GCA_016708875.1_ASM1670887v1_genomic.fna/cds.fna -a GCA_016708875.1_ASM1670887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:12:16,740] [INFO] Task succeeded: Prodigal
[2023-06-30 04:12:16,740] [INFO] Task started: HMMsearch
[2023-06-30 04:12:16,740] [INFO] Running command: hmmsearch --tblout GCA_016708875.1_ASM1670887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference/reference_markers.hmm GCA_016708875.1_ASM1670887v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:12:17,067] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:12:17,069] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5feaa4cf-ca05-4862-9343-ddc867f37303/GCA_016708875.1_ASM1670887v1_genomic.fna.gz]
[2023-06-30 04:12:17,123] [INFO] Query marker FASTA was written to GCA_016708875.1_ASM1670887v1_genomic.fna/markers.fasta
[2023-06-30 04:12:17,123] [INFO] Task started: Blastn
[2023-06-30 04:12:17,124] [INFO] Running command: blastn -query GCA_016708875.1_ASM1670887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference/reference_markers.fasta -out GCA_016708875.1_ASM1670887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:12:17,693] [INFO] Task succeeded: Blastn
[2023-06-30 04:12:17,697] [INFO] Selected 22 target genomes.
[2023-06-30 04:12:17,697] [INFO] Target genome list was writen to GCA_016708875.1_ASM1670887v1_genomic.fna/target_genomes.txt
[2023-06-30 04:12:17,698] [INFO] Task started: fastANI
[2023-06-30 04:12:17,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg5feaa4cf-ca05-4862-9343-ddc867f37303/GCA_016708875.1_ASM1670887v1_genomic.fna.gz --refList GCA_016708875.1_ASM1670887v1_genomic.fna/target_genomes.txt --output GCA_016708875.1_ASM1670887v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:12:34,008] [INFO] Task succeeded: fastANI
[2023-06-30 04:12:34,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:12:34,008] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:12:34,010] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:12:34,010] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:12:34,011] [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
--------------------------------------------------------------------------------
[2023-06-30 04:12:34,013] [INFO] DFAST Taxonomy check result was written to GCA_016708875.1_ASM1670887v1_genomic.fna/tc_result.tsv
[2023-06-30 04:12:34,013] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:12:34,013] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:12:34,013] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference/checkm_data
[2023-06-30 04:12:34,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:12:34,075] [INFO] Task started: CheckM
[2023-06-30 04:12:34,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708875.1_ASM1670887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708875.1_ASM1670887v1_genomic.fna/checkm_input GCA_016708875.1_ASM1670887v1_genomic.fna/checkm_result
[2023-06-30 04:14:14,605] [INFO] Task succeeded: CheckM
[2023-06-30 04:14:14,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 04:14:14,634] [INFO] ===== Completeness check finished =====
[2023-06-30 04:14:14,635] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:14:14,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708875.1_ASM1670887v1_genomic.fna/markers.fasta)
[2023-06-30 04:14:14,636] [INFO] Task started: Blastn
[2023-06-30 04:14:14,636] [INFO] Running command: blastn -query GCA_016708875.1_ASM1670887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg671cb0f0-fcd0-4732-80bc-c35e24f031dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708875.1_ASM1670887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:14:15,385] [INFO] Task succeeded: Blastn
[2023-06-30 04:14:15,389] [INFO] Selected 15 target genomes.
[2023-06-30 04:14:15,389] [INFO] Target genome list was writen to GCA_016708875.1_ASM1670887v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:14:15,393] [INFO] Task started: fastANI
[2023-06-30 04:14:15,393] [INFO] Running command: fastANI --query /var/lib/cwl/stg5feaa4cf-ca05-4862-9343-ddc867f37303/GCA_016708875.1_ASM1670887v1_genomic.fna.gz --refList GCA_016708875.1_ASM1670887v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708875.1_ASM1670887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:14:30,200] [INFO] Task succeeded: fastANI
[2023-06-30 04:14:30,211] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:14:30,211] [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_016708875.1	s__M3007 sp016708875	100.0	2016	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014379065.1	s__M3007 sp014379065	79.6433	756	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303475.1	s__M3007 sp017303475	77.0791	298	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711435.1	s__M3007 sp016711435	76.8438	197	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787545.1	s__M3007 sp016787545	76.7523	250	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713985.1	s__M3007 sp016713985	76.5542	197	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331955.1	s__M3007 sp011331955	76.4713	189	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187225.1	s__M3007 sp019187225	76.2904	214	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712415.1	s__M3007 sp016712415	76.2469	170	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787415.1	s__M3007 sp016787415	76.0913	168	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787345.1	s__M3007 sp016787345	76.0459	127	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303875.1	s__M3007 sp017303875	75.6423	123	2023	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__M3007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 04:14:30,213] [INFO] GTDB search result was written to GCA_016708875.1_ASM1670887v1_genomic.fna/result_gtdb.tsv
[2023-06-30 04:14:30,214] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:14:30,217] [INFO] DFAST_QC result json was written to GCA_016708875.1_ASM1670887v1_genomic.fna/dqc_result.json
[2023-06-30 04:14:30,217] [INFO] DFAST_QC completed!
[2023-06-30 04:14:30,217] [INFO] Total running time: 0h2m52s