[2023-06-29 14:32:01,902] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:32:01,904] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:32:01,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference
[2023-06-29 14:32:03,338] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:32:03,339] [INFO] Task started: Prodigal
[2023-06-29 14:32:03,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg77c9b1b3-bb37-447d-8a3a-50bc04ecd107/GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:32:06,777] [INFO] Task succeeded: Prodigal
[2023-06-29 14:32:06,778] [INFO] Task started: HMMsearch
[2023-06-29 14:32:06,778] [INFO] Running command: hmmsearch --tblout GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference/reference_markers.hmm GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:32:07,017] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:32:07,019] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77c9b1b3-bb37-447d-8a3a-50bc04ecd107/GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 14:32:07,045] [INFO] Query marker FASTA was written to GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 14:32:07,045] [INFO] Task started: Blastn
[2023-06-29 14:32:07,046] [INFO] Running command: blastn -query GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference/reference_markers.fasta -out GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:32:07,636] [INFO] Task succeeded: Blastn
[2023-06-29 14:32:07,640] [INFO] Selected 20 target genomes.
[2023-06-29 14:32:07,641] [INFO] Target genome list was writen to GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 14:32:07,645] [INFO] Task started: fastANI
[2023-06-29 14:32:07,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c9b1b3-bb37-447d-8a3a-50bc04ecd107/GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:32:16,668] [INFO] Task succeeded: fastANI
[2023-06-29 14:32:16,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:32:16,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:32:16,670] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:32:16,670] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 14:32:16,671] [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 14:32:16,673] [INFO] DFAST Taxonomy check result was written to GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 14:32:16,674] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:32:16,674] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:32:16,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference/checkm_data
[2023-06-29 14:32:16,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:32:16,702] [INFO] Task started: CheckM
[2023-06-29 14:32:16,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 14:32:35,016] [INFO] Task succeeded: CheckM
[2023-06-29 14:32:35,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:32:35,039] [INFO] ===== Completeness check finished =====
[2023-06-29 14:32:35,039] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:32:35,040] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 14:32:35,040] [INFO] Task started: Blastn
[2023-06-29 14:32:35,040] [INFO] Running command: blastn -query GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d68a99-ce33-449e-9d62-eda151f43b8c/dqc_reference/reference_markers_gtdb.fasta -out GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:32:35,859] [INFO] Task succeeded: Blastn
[2023-06-29 14:32:35,868] [INFO] Selected 19 target genomes.
[2023-06-29 14:32:35,868] [INFO] Target genome list was writen to GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:32:35,882] [INFO] Task started: fastANI
[2023-06-29 14:32:35,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg77c9b1b3-bb37-447d-8a3a-50bc04ecd107/GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:32:43,174] [INFO] Task succeeded: fastANI
[2023-06-29 14:32:43,204] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:32:43,205] [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_018674095.1	s__GCA-2722105 sp018674095	96.2361	363	454	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	conclusive
GCA_018692355.1	s__GCA-2722105 sp018692355	79.2477	163	454	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.23	99.02	0.79	0.73	14	-
GCA_015658495.1	s__GCA-2722105 sp015658495	78.3213	114	454	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018649625.1	s__GCA-2722105 sp018649625	77.3705	142	454	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
GCA_002722105.1	s__GCA-2722105 sp002722105	76.2176	64	454	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:32:43,207] [INFO] GTDB search result was written to GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 14:32:43,208] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:32:43,211] [INFO] DFAST_QC result json was written to GCA_937893045.1_ERR2206762_bin.129_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 14:32:43,212] [INFO] DFAST_QC completed!
[2023-06-29 14:32:43,212] [INFO] Total running time: 0h0m41s