[2023-03-19 02:05:13,301] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:13,302] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:13,302] [INFO] DQC Reference Directory: /var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference
[2023-03-19 02:05:14,439] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:14,440] [INFO] Task started: Prodigal
[2023-03-19 02:05:14,440] [INFO] Running command: cat /var/lib/cwl/stgabbc1dc5-4475-49e0-ae31-764ed56c6846/OceanDNA-b45252.fa | prodigal -d OceanDNA-b45252/cds.fna -a OceanDNA-b45252/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:36,952] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:36,953] [INFO] Task started: HMMsearch
[2023-03-19 02:05:36,953] [INFO] Running command: hmmsearch --tblout OceanDNA-b45252/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference/reference_markers.hmm OceanDNA-b45252/protein.faa > /dev/null
[2023-03-19 02:05:37,189] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:37,189] [INFO] Found 6/6 markers.
[2023-03-19 02:05:37,214] [INFO] Query marker FASTA was written to OceanDNA-b45252/markers.fasta
[2023-03-19 02:05:37,215] [INFO] Task started: Blastn
[2023-03-19 02:05:37,215] [INFO] Running command: blastn -query OceanDNA-b45252/markers.fasta -db /var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference/reference_markers.fasta -out OceanDNA-b45252/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:37,759] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:37,759] [INFO] Selected 19 target genomes.
[2023-03-19 02:05:37,760] [INFO] Target genome list was writen to OceanDNA-b45252/target_genomes.txt
[2023-03-19 02:05:37,771] [INFO] Task started: fastANI
[2023-03-19 02:05:37,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgabbc1dc5-4475-49e0-ae31-764ed56c6846/OceanDNA-b45252.fa --refList OceanDNA-b45252/target_genomes.txt --output OceanDNA-b45252/fastani_result.tsv --threads 1
[2023-03-19 02:05:52,894] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:52,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:52,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:52,898] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:52,898] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:05:52,898] [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
Micromonospora echinaurantiaca	strain=DSM 43904	GCA_900090235.1	47857	47857	type	True	74.7479	66	1215	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.6867	61	1215	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:05:52,898] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45252/tc_result.tsv
[2023-03-19 02:05:52,898] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:52,898] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:52,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference/checkm_data
[2023-03-19 02:05:52,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:52,904] [INFO] Task started: CheckM
[2023-03-19 02:05:52,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45252/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45252/checkm_input OceanDNA-b45252/checkm_result
[2023-03-19 02:06:48,612] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:48,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:48,614] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:48,615] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:48,615] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45252/markers.fasta)
[2023-03-19 02:06:48,616] [INFO] Task started: Blastn
[2023-03-19 02:06:48,616] [INFO] Running command: blastn -query OceanDNA-b45252/markers.fasta -db /var/lib/cwl/stga841ea73-16c2-4897-bfd0-165b805677af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45252/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:49,377] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:49,378] [INFO] Selected 19 target genomes.
[2023-03-19 02:06:49,378] [INFO] Target genome list was writen to OceanDNA-b45252/target_genomes_gtdb.txt
[2023-03-19 02:06:49,712] [INFO] Task started: fastANI
[2023-03-19 02:06:49,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgabbc1dc5-4475-49e0-ae31-764ed56c6846/OceanDNA-b45252.fa --refList OceanDNA-b45252/target_genomes_gtdb.txt --output OceanDNA-b45252/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:07:00,503] [INFO] Task succeeded: fastANI
[2023-03-19 02:07:00,508] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:07:00,508] [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_002313505.1	s__Alkalispirochaeta sp002313505	99.7827	1029	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007130865.1	s__Alkalispirochaeta sp007130865	76.6069	116	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	99.39	99.33	0.88	0.87	3	-
GCA_007695175.1	s__Alkalispirochaeta sp007695175	76.5066	112	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117185.1	s__Alkalispirochaeta sp007117185	76.4897	131	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156105.1	s__Alkalispirochaeta americana	76.2694	68	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__Alkalispirochaetaceae;g__Alkalispirochaeta	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693485.1	s__PWMO01 sp007693485	76.2082	62	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__DSM-27196;f__PWMO01;g__PWMO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262985.1	s__JAFGNN01 sp018262985	75.5983	60	1215	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	98.32	98.32	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-19 02:07:00,508] [INFO] GTDB search result was written to OceanDNA-b45252/result_gtdb.tsv
[2023-03-19 02:07:00,508] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:07:00,509] [INFO] DFAST_QC result json was written to OceanDNA-b45252/dqc_result.json
[2023-03-19 02:07:00,509] [INFO] DFAST_QC completed!
[2023-03-19 02:07:00,509] [INFO] Total running time: 0h1m47s