[2023-03-16 04:54:07,049] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,049] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,049] [INFO] DQC Reference Directory: /var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference
[2023-03-16 04:54:08,370] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,370] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,370] [INFO] Running command: cat /var/lib/cwl/stgb33be846-c7de-4ed3-b190-7a797cbd8aa9/OceanDNA-a2728.fa | prodigal -d OceanDNA-a2728/cds.fna -a OceanDNA-a2728/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:18,513] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:18,514] [INFO] Task started: HMMsearch
[2023-03-16 04:54:18,514] [INFO] Running command: hmmsearch --tblout OceanDNA-a2728/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference/reference_markers.hmm OceanDNA-a2728/protein.faa > /dev/null
[2023-03-16 04:54:18,733] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:18,734] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb33be846-c7de-4ed3-b190-7a797cbd8aa9/OceanDNA-a2728.fa]
[2023-03-16 04:54:18,747] [INFO] Query marker FASTA was written to OceanDNA-a2728/markers.fasta
[2023-03-16 04:54:18,748] [INFO] Task started: Blastn
[2023-03-16 04:54:18,748] [INFO] Running command: blastn -query OceanDNA-a2728/markers.fasta -db /var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference/reference_markers.fasta -out OceanDNA-a2728/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:19,222] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:19,223] [INFO] Selected 5 target genomes.
[2023-03-16 04:54:19,223] [INFO] Target genome list was writen to OceanDNA-a2728/target_genomes.txt
[2023-03-16 04:54:19,226] [INFO] Task started: fastANI
[2023-03-16 04:54:19,226] [INFO] Running command: fastANI --query /var/lib/cwl/stgb33be846-c7de-4ed3-b190-7a797cbd8aa9/OceanDNA-a2728.fa --refList OceanDNA-a2728/target_genomes.txt --output OceanDNA-a2728/fastani_result.tsv --threads 1
[2023-03-16 04:54:22,302] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:22,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:22,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:22,302] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:22,302] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 04:54:22,302] [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
--------------------------------------------------------------------------------
[2023-03-16 04:54:22,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2728/tc_result.tsv
[2023-03-16 04:54:22,303] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:22,303] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:22,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference/checkm_data
[2023-03-16 04:54:22,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:22,333] [INFO] Task started: CheckM
[2023-03-16 04:54:22,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2728/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2728/checkm_input OceanDNA-a2728/checkm_result
[2023-03-16 04:54:53,892] [INFO] Task succeeded: CheckM
[2023-03-16 04:54:53,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.34%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:54:53,895] [INFO] ===== Completeness check finished =====
[2023-03-16 04:54:53,895] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:54:53,895] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2728/markers.fasta)
[2023-03-16 04:54:53,896] [INFO] Task started: Blastn
[2023-03-16 04:54:53,896] [INFO] Running command: blastn -query OceanDNA-a2728/markers.fasta -db /var/lib/cwl/stga1f7bd60-3c78-4050-bf54-3963c6fb470d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2728/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:54,343] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:54,344] [INFO] Selected 9 target genomes.
[2023-03-16 04:54:54,344] [INFO] Target genome list was writen to OceanDNA-a2728/target_genomes_gtdb.txt
[2023-03-16 04:54:54,354] [INFO] Task started: fastANI
[2023-03-16 04:54:54,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgb33be846-c7de-4ed3-b190-7a797cbd8aa9/OceanDNA-a2728.fa --refList OceanDNA-a2728/target_genomes_gtdb.txt --output OceanDNA-a2728/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:54:56,965] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:56,970] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:54:56,970] [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_002719815.1	s__MGIIa-L2 sp002719815	78.872	206	501	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499195.1	s__MGIIa-L2 sp002499195	78.6507	261	501	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	-
GCA_002706065.1	s__MGIIa-L2 sp002706065	78.3372	236	501	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002502215.1	s__MGIIa-L2 sp002502215	78.1627	206	501	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.03	97.17	0.84	0.82	4	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	76.9292	94	501	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:54:56,970] [INFO] GTDB search result was written to OceanDNA-a2728/result_gtdb.tsv
[2023-03-16 04:54:56,971] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:54:56,971] [INFO] DFAST_QC result json was written to OceanDNA-a2728/dqc_result.json
[2023-03-16 04:54:56,971] [INFO] DFAST_QC completed!
[2023-03-16 04:54:56,971] [INFO] Total running time: 0h0m50s