[2023-03-18 00:53:42,860] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,861] [INFO] DQC Reference Directory: /var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference
[2023-03-18 00:53:44,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,409] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,409] [INFO] Running command: cat /var/lib/cwl/stg62177377-0963-44d6-8383-f0834401a49d/OceanDNA-b21025.fa | prodigal -d OceanDNA-b21025/cds.fna -a OceanDNA-b21025/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:05,814] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:05,814] [INFO] Task started: HMMsearch
[2023-03-18 00:54:05,814] [INFO] Running command: hmmsearch --tblout OceanDNA-b21025/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference/reference_markers.hmm OceanDNA-b21025/protein.faa > /dev/null
[2023-03-18 00:54:06,005] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:06,006] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg62177377-0963-44d6-8383-f0834401a49d/OceanDNA-b21025.fa]
[2023-03-18 00:54:06,033] [INFO] Query marker FASTA was written to OceanDNA-b21025/markers.fasta
[2023-03-18 00:54:06,033] [INFO] Task started: Blastn
[2023-03-18 00:54:06,033] [INFO] Running command: blastn -query OceanDNA-b21025/markers.fasta -db /var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference/reference_markers.fasta -out OceanDNA-b21025/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:06,554] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:06,555] [INFO] Selected 15 target genomes.
[2023-03-18 00:54:06,555] [INFO] Target genome list was writen to OceanDNA-b21025/target_genomes.txt
[2023-03-18 00:54:06,565] [INFO] Task started: fastANI
[2023-03-18 00:54:06,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg62177377-0963-44d6-8383-f0834401a49d/OceanDNA-b21025.fa --refList OceanDNA-b21025/target_genomes.txt --output OceanDNA-b21025/fastani_result.tsv --threads 1
[2023-03-18 00:54:15,047] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:15,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:15,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:15,048] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:15,048] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:54:15,048] [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
--------------------------------------------------------------------------------
[2023-03-18 00:54:15,048] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21025/tc_result.tsv
[2023-03-18 00:54:15,048] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:15,049] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:15,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference/checkm_data
[2023-03-18 00:54:15,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:15,057] [INFO] Task started: CheckM
[2023-03-18 00:54:15,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21025/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21025/checkm_input OceanDNA-b21025/checkm_result
[2023-03-18 00:55:09,217] [INFO] Task succeeded: CheckM
[2023-03-18 00:55:09,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:55:09,221] [INFO] ===== Completeness check finished =====
[2023-03-18 00:55:09,221] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:55:09,221] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21025/markers.fasta)
[2023-03-18 00:55:09,221] [INFO] Task started: Blastn
[2023-03-18 00:55:09,221] [INFO] Running command: blastn -query OceanDNA-b21025/markers.fasta -db /var/lib/cwl/stga9dba670-3a92-4927-ad65-107914271311/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21025/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:55:09,950] [INFO] Task succeeded: Blastn
[2023-03-18 00:55:09,950] [INFO] Selected 9 target genomes.
[2023-03-18 00:55:09,950] [INFO] Target genome list was writen to OceanDNA-b21025/target_genomes_gtdb.txt
[2023-03-18 00:55:09,960] [INFO] Task started: fastANI
[2023-03-18 00:55:09,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg62177377-0963-44d6-8383-f0834401a49d/OceanDNA-b21025.fa --refList OceanDNA-b21025/target_genomes_gtdb.txt --output OceanDNA-b21025/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:16,657] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:16,662] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:55:16,662] [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_002390675.1	s__UBA4427 sp002390675	93.8521	1003	1184	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	99.70	99.70	0.94	0.94	2	-
GCA_002709835.1	s__UBA4427 sp002709835	77.2411	241	1184	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719955.1	s__UBA4427 sp002719955	77.0195	236	1184	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959805.1	s__UBA4427 sp012959805	76.9438	112	1184	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	99.86	99.86	0.88	0.88	2	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.5053	218	1184	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051925.1	s__UBA4427 sp011051925	76.383	131	1184	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:55:16,662] [INFO] GTDB search result was written to OceanDNA-b21025/result_gtdb.tsv
[2023-03-18 00:55:16,663] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:16,663] [INFO] DFAST_QC result json was written to OceanDNA-b21025/dqc_result.json
[2023-03-18 00:55:16,663] [INFO] DFAST_QC completed!
[2023-03-18 00:55:16,664] [INFO] Total running time: 0h1m34s