[2023-03-17 07:44:36,994] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,994] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference
[2023-03-17 07:44:38,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,850] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,850] [INFO] Running command: cat /var/lib/cwl/stgf36b0764-95c3-4dad-a826-9d43a3bc5688/OceanDNA-b15507.fa | prodigal -d OceanDNA-b15507/cds.fna -a OceanDNA-b15507/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:54,676] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:54,676] [INFO] Task started: HMMsearch
[2023-03-17 07:44:54,676] [INFO] Running command: hmmsearch --tblout OceanDNA-b15507/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference/reference_markers.hmm OceanDNA-b15507/protein.faa > /dev/null
[2023-03-17 07:44:54,846] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:54,847] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf36b0764-95c3-4dad-a826-9d43a3bc5688/OceanDNA-b15507.fa]
[2023-03-17 07:44:54,868] [INFO] Query marker FASTA was written to OceanDNA-b15507/markers.fasta
[2023-03-17 07:44:54,868] [INFO] Task started: Blastn
[2023-03-17 07:44:54,868] [INFO] Running command: blastn -query OceanDNA-b15507/markers.fasta -db /var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference/reference_markers.fasta -out OceanDNA-b15507/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:55,389] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:55,390] [INFO] Selected 12 target genomes.
[2023-03-17 07:44:55,390] [INFO] Target genome list was writen to OceanDNA-b15507/target_genomes.txt
[2023-03-17 07:44:55,397] [INFO] Task started: fastANI
[2023-03-17 07:44:55,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgf36b0764-95c3-4dad-a826-9d43a3bc5688/OceanDNA-b15507.fa --refList OceanDNA-b15507/target_genomes.txt --output OceanDNA-b15507/fastani_result.tsv --threads 1
[2023-03-17 07:45:05,791] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:05,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:05,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:05,792] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:05,792] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:45:05,792] [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
--------------------------------------------------------------------------------
[2023-03-17 07:45:05,792] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15507/tc_result.tsv
[2023-03-17 07:45:05,792] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:05,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:05,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference/checkm_data
[2023-03-17 07:45:05,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:05,800] [INFO] Task started: CheckM
[2023-03-17 07:45:05,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15507/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15507/checkm_input OceanDNA-b15507/checkm_result
[2023-03-17 07:45:47,637] [INFO] Task succeeded: CheckM
[2023-03-17 07:45:47,638] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:45:47,640] [INFO] ===== Completeness check finished =====
[2023-03-17 07:45:47,641] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:45:47,641] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15507/markers.fasta)
[2023-03-17 07:45:47,641] [INFO] Task started: Blastn
[2023-03-17 07:45:47,641] [INFO] Running command: blastn -query OceanDNA-b15507/markers.fasta -db /var/lib/cwl/stg2a2e93a8-00b9-4896-89d0-e304f6895296/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15507/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:48,364] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:48,365] [INFO] Selected 18 target genomes.
[2023-03-17 07:45:48,365] [INFO] Target genome list was writen to OceanDNA-b15507/target_genomes_gtdb.txt
[2023-03-17 07:45:48,399] [INFO] Task started: fastANI
[2023-03-17 07:45:48,399] [INFO] Running command: fastANI --query /var/lib/cwl/stgf36b0764-95c3-4dad-a826-9d43a3bc5688/OceanDNA-b15507.fa --refList OceanDNA-b15507/target_genomes_gtdb.txt --output OceanDNA-b15507/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:45:57,300] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:57,306] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:45:57,306] [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_002816875.1	s__Io17-Chloro-G2 sp002816875	80.4035	281	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Io17-Chloro-G2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401285.1	s__UBA11650 sp002401285	76.685	90	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	98.75	98.75	0.80	0.80	2	-
GCA_002710215.1	s__UBA11650 sp002710215	76.4247	97	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	99.22	99.06	0.76	0.73	3	-
GCA_009692925.1	s__SHYG01 sp009692925	75.8931	68	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	99.84	99.84	0.93	0.93	2	-
GCA_002238825.1	s__Bin87 sp002238825	75.8597	71	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840175.1	s__VXOI01 sp009840175	75.8543	65	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__VXOI01	95.0	99.70	99.70	0.91	0.91	2	-
GCA_016872385.1	s__SHYG01 sp016872385	75.7652	63	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840135.1	s__Bin22 sp009840135	75.5586	56	829	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:45:57,306] [INFO] GTDB search result was written to OceanDNA-b15507/result_gtdb.tsv
[2023-03-17 07:45:57,307] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:45:57,307] [INFO] DFAST_QC result json was written to OceanDNA-b15507/dqc_result.json
[2023-03-17 07:45:57,307] [INFO] DFAST_QC completed!
[2023-03-17 07:45:57,307] [INFO] Total running time: 0h1m20s