[2023-03-18 04:16:54,163] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:54,164] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:54,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference
[2023-03-18 04:16:55,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:55,826] [INFO] Task started: Prodigal
[2023-03-18 04:16:55,826] [INFO] Running command: cat /var/lib/cwl/stgec45b437-4e57-43a1-9f4a-16385c835a23/OceanDNA-a1822.fa | prodigal -d OceanDNA-a1822/cds.fna -a OceanDNA-a1822/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:16:59,057] [INFO] Task succeeded: Prodigal
[2023-03-18 04:16:59,058] [INFO] Task started: HMMsearch
[2023-03-18 04:16:59,058] [INFO] Running command: hmmsearch --tblout OceanDNA-a1822/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference/reference_markers.hmm OceanDNA-a1822/protein.faa > /dev/null
[2023-03-18 04:16:59,246] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:16:59,246] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgec45b437-4e57-43a1-9f4a-16385c835a23/OceanDNA-a1822.fa]
[2023-03-18 04:16:59,256] [INFO] Query marker FASTA was written to OceanDNA-a1822/markers.fasta
[2023-03-18 04:16:59,257] [INFO] Task started: Blastn
[2023-03-18 04:16:59,257] [INFO] Running command: blastn -query OceanDNA-a1822/markers.fasta -db /var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference/reference_markers.fasta -out OceanDNA-a1822/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:01,794] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:01,795] [INFO] Selected 1 target genomes.
[2023-03-18 04:17:01,795] [INFO] Target genome list was writen to OceanDNA-a1822/target_genomes.txt
[2023-03-18 04:17:01,796] [INFO] Task started: fastANI
[2023-03-18 04:17:01,797] [INFO] Running command: fastANI --query /var/lib/cwl/stgec45b437-4e57-43a1-9f4a-16385c835a23/OceanDNA-a1822.fa --refList OceanDNA-a1822/target_genomes.txt --output OceanDNA-a1822/fastani_result.tsv --threads 1
[2023-03-18 04:17:02,394] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:02,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:02,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:02,395] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:02,395] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 04:17:02,395] [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 04:17:02,395] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1822/tc_result.tsv
[2023-03-18 04:17:02,395] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:02,395] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:02,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference/checkm_data
[2023-03-18 04:17:02,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:02,408] [INFO] Task started: CheckM
[2023-03-18 04:17:02,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1822/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1822/checkm_input OceanDNA-a1822/checkm_result
[2023-03-18 04:17:19,751] [INFO] Task succeeded: CheckM
[2023-03-18 04:17:19,751] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.62%
Contamintation: 3.12%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:17:19,753] [INFO] ===== Completeness check finished =====
[2023-03-18 04:17:19,753] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:17:19,753] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1822/markers.fasta)
[2023-03-18 04:17:19,755] [INFO] Task started: Blastn
[2023-03-18 04:17:19,755] [INFO] Running command: blastn -query OceanDNA-a1822/markers.fasta -db /var/lib/cwl/stg2b42b135-ad73-456b-b93e-96e650af981e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1822/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:20,371] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:20,372] [INFO] Selected 9 target genomes.
[2023-03-18 04:17:20,372] [INFO] Target genome list was writen to OceanDNA-a1822/target_genomes_gtdb.txt
[2023-03-18 04:17:20,377] [INFO] Task started: fastANI
[2023-03-18 04:17:20,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgec45b437-4e57-43a1-9f4a-16385c835a23/OceanDNA-a1822.fa --refList OceanDNA-a1822/target_genomes_gtdb.txt --output OceanDNA-a1822/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:17:22,724] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:22,728] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:17:22,728] [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_002696315.1	s__MGIIa-I sp002696315	92.4779	119	132	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.61	99.61	0.93	0.93	2	-
GCA_002498205.1	s__MGIIa-I sp002498205	84.3328	101	132	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692465.1	s__MGIIa-I sp002692465	82.5749	103	132	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720275.1	s__MGIIa-I sp002720275	81.7531	110	132	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	98.73	98.73	0.82	0.82	2	-
GCA_002720095.2	s__MGIIa-I sp002720095	78.2843	50	132	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-I	95.0	99.78	99.77	0.92	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-18 04:17:22,728] [INFO] GTDB search result was written to OceanDNA-a1822/result_gtdb.tsv
[2023-03-18 04:17:22,728] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:17:22,729] [INFO] DFAST_QC result json was written to OceanDNA-a1822/dqc_result.json
[2023-03-18 04:17:22,729] [INFO] DFAST_QC completed!
[2023-03-18 04:17:22,729] [INFO] Total running time: 0h0m29s