[2023-06-18 21:35:30,386] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:35:30,389] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:35:30,390] [INFO] DQC Reference Directory: /var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference
[2023-06-18 21:35:32,680] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:35:32,682] [INFO] Task started: Prodigal
[2023-06-18 21:35:32,683] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7e8a7be-a206-45ff-a035-e0a2ee19b8c7/GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:35:41,388] [INFO] Task succeeded: Prodigal
[2023-06-18 21:35:41,389] [INFO] Task started: HMMsearch
[2023-06-18 21:35:41,389] [INFO] Running command: hmmsearch --tblout GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference/reference_markers.hmm GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:35:41,656] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:35:41,658] [INFO] Found 6/6 markers.
[2023-06-18 21:35:41,691] [INFO] Query marker FASTA was written to GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 21:35:41,691] [INFO] Task started: Blastn
[2023-06-18 21:35:41,691] [INFO] Running command: blastn -query GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference/reference_markers.fasta -out GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:35:42,272] [INFO] Task succeeded: Blastn
[2023-06-18 21:35:42,280] [INFO] Selected 22 target genomes.
[2023-06-18 21:35:42,281] [INFO] Target genome list was writen to GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 21:35:42,286] [INFO] Task started: fastANI
[2023-06-18 21:35:42,286] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7e8a7be-a206-45ff-a035-e0a2ee19b8c7/GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:35:53,861] [INFO] Task succeeded: fastANI
[2023-06-18 21:35:53,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:35:53,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:35:53,863] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:35:53,864] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:35:53,864] [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
--------------------------------------------------------------------------------
[2023-06-18 21:35:53,869] [INFO] DFAST Taxonomy check result was written to GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 21:35:53,870] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:35:53,870] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:35:53,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference/checkm_data
[2023-06-18 21:35:53,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:35:53,912] [INFO] Task started: CheckM
[2023-06-18 21:35:53,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 21:36:25,572] [INFO] Task succeeded: CheckM
[2023-06-18 21:36:25,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:36:25,602] [INFO] ===== Completeness check finished =====
[2023-06-18 21:36:25,603] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:36:25,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 21:36:25,605] [INFO] Task started: Blastn
[2023-06-18 21:36:25,605] [INFO] Running command: blastn -query GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga82d4e47-9f36-4d34-bdc0-a468e822e1e2/dqc_reference/reference_markers_gtdb.fasta -out GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:36:26,418] [INFO] Task succeeded: Blastn
[2023-06-18 21:36:26,430] [INFO] Selected 17 target genomes.
[2023-06-18 21:36:26,430] [INFO] Target genome list was writen to GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:36:26,433] [INFO] Task started: fastANI
[2023-06-18 21:36:26,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7e8a7be-a206-45ff-a035-e0a2ee19b8c7/GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:36:34,540] [INFO] Task succeeded: fastANI
[2023-06-18 21:36:34,557] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:36:34,558] [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_003519545.1	s__UBA9002 sp003519545	99.6402	637	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA9002	95.0	97.76	96.51	0.82	0.75	3	conclusive
GCA_002455255.1	s__UBA9002 sp002455255	80.504	532	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA9002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266835.1	s__JAFDZO01 sp018266835	75.6118	81	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAFDZO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719565.1	s__UBA2330 sp016719565	75.5278	65	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA2330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710985.1	s__JAGPCH01 sp016710985	75.5013	61	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAGPCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266845.1	s__JAFDZO01 sp018266845	75.4551	56	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAFDZO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788375.1	s__JAEUSI01 sp016788375	75.379	52	819	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAEUSI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:36:34,561] [INFO] GTDB search result was written to GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 21:36:34,561] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:36:34,566] [INFO] DFAST_QC result json was written to GCA_937982465.1_SRR1506984_bin.108_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 21:36:34,566] [INFO] DFAST_QC completed!
[2023-06-18 21:36:34,566] [INFO] Total running time: 0h1m4s