[2023-03-17 03:28:37,116] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:28:37,116] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:28:37,116] [INFO] DQC Reference Directory: /var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference
[2023-03-17 03:28:38,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:28:38,270] [INFO] Task started: Prodigal
[2023-03-17 03:28:38,270] [INFO] Running command: cat /var/lib/cwl/stg0862102a-f868-41bb-a653-f8cd89a45e0a/OceanDNA-b20508.fa | prodigal -d OceanDNA-b20508/cds.fna -a OceanDNA-b20508/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:28:43,089] [INFO] Task succeeded: Prodigal
[2023-03-17 03:28:43,089] [INFO] Task started: HMMsearch
[2023-03-17 03:28:43,089] [INFO] Running command: hmmsearch --tblout OceanDNA-b20508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference/reference_markers.hmm OceanDNA-b20508/protein.faa > /dev/null
[2023-03-17 03:28:43,241] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:28:43,242] [INFO] Found 6/6 markers.
[2023-03-17 03:28:43,251] [INFO] Query marker FASTA was written to OceanDNA-b20508/markers.fasta
[2023-03-17 03:28:43,252] [INFO] Task started: Blastn
[2023-03-17 03:28:43,252] [INFO] Running command: blastn -query OceanDNA-b20508/markers.fasta -db /var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference/reference_markers.fasta -out OceanDNA-b20508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:28:43,761] [INFO] Task succeeded: Blastn
[2023-03-17 03:28:43,761] [INFO] Selected 11 target genomes.
[2023-03-17 03:28:43,761] [INFO] Target genome list was writen to OceanDNA-b20508/target_genomes.txt
[2023-03-17 03:28:43,769] [INFO] Task started: fastANI
[2023-03-17 03:28:43,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg0862102a-f868-41bb-a653-f8cd89a45e0a/OceanDNA-b20508.fa --refList OceanDNA-b20508/target_genomes.txt --output OceanDNA-b20508/fastani_result.tsv --threads 1
[2023-03-17 03:28:49,611] [INFO] Task succeeded: fastANI
[2023-03-17 03:28:49,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:28:49,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:28:49,612] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:28:49,612] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:28:49,612] [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 03:28:49,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20508/tc_result.tsv
[2023-03-17 03:28:49,612] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:28:49,612] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:28:49,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference/checkm_data
[2023-03-17 03:28:49,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:28:49,900] [INFO] Task started: CheckM
[2023-03-17 03:28:49,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20508/checkm_input OceanDNA-b20508/checkm_result
[2023-03-17 03:29:08,060] [INFO] Task succeeded: CheckM
[2023-03-17 03:29:08,060] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.23%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:29:08,062] [INFO] ===== Completeness check finished =====
[2023-03-17 03:29:08,062] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:29:08,062] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20508/markers.fasta)
[2023-03-17 03:29:08,064] [INFO] Task started: Blastn
[2023-03-17 03:29:08,064] [INFO] Running command: blastn -query OceanDNA-b20508/markers.fasta -db /var/lib/cwl/stg95273a61-1cdd-49e6-a7e4-48c12204f1b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:08,971] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:08,972] [INFO] Selected 25 target genomes.
[2023-03-17 03:29:08,972] [INFO] Target genome list was writen to OceanDNA-b20508/target_genomes_gtdb.txt
[2023-03-17 03:29:08,993] [INFO] Task started: fastANI
[2023-03-17 03:29:08,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg0862102a-f868-41bb-a653-f8cd89a45e0a/OceanDNA-b20508.fa --refList OceanDNA-b20508/target_genomes_gtdb.txt --output OceanDNA-b20508/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:29:15,826] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:15,829] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:29:15,829] [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_002693365.1	s__GCA-002707645 sp002693365	76.18	57	321	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
GCA_002705605.1	s__GCA-002707645 sp002705605	76.1153	72	321	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707645.1	s__GCA-002707645 sp002707645	76.0464	52	321	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:29:15,830] [INFO] GTDB search result was written to OceanDNA-b20508/result_gtdb.tsv
[2023-03-17 03:29:15,830] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:29:15,830] [INFO] DFAST_QC result json was written to OceanDNA-b20508/dqc_result.json
[2023-03-17 03:29:15,830] [INFO] DFAST_QC completed!
[2023-03-17 03:29:15,830] [INFO] Total running time: 0h0m39s