[2023-03-16 05:27:24,042] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:27:24,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:27:24,042] [INFO] DQC Reference Directory: /var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference
[2023-03-16 05:27:25,179] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:27:25,179] [INFO] Task started: Prodigal
[2023-03-16 05:27:25,179] [INFO] Running command: cat /var/lib/cwl/stge8ddbd28-17e1-4a77-9e65-f681f5fd8c38/OceanDNA-b17183.fa | prodigal -d OceanDNA-b17183/cds.fna -a OceanDNA-b17183/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:27:36,894] [INFO] Task succeeded: Prodigal
[2023-03-16 05:27:36,894] [INFO] Task started: HMMsearch
[2023-03-16 05:27:36,894] [INFO] Running command: hmmsearch --tblout OceanDNA-b17183/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference/reference_markers.hmm OceanDNA-b17183/protein.faa > /dev/null
[2023-03-16 05:27:37,097] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:27:37,098] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge8ddbd28-17e1-4a77-9e65-f681f5fd8c38/OceanDNA-b17183.fa]
[2023-03-16 05:27:37,142] [INFO] Query marker FASTA was written to OceanDNA-b17183/markers.fasta
[2023-03-16 05:27:37,144] [INFO] Task started: Blastn
[2023-03-16 05:27:37,144] [INFO] Running command: blastn -query OceanDNA-b17183/markers.fasta -db /var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference/reference_markers.fasta -out OceanDNA-b17183/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:27:37,641] [INFO] Task succeeded: Blastn
[2023-03-16 05:27:37,645] [INFO] Selected 13 target genomes.
[2023-03-16 05:27:37,646] [INFO] Target genome list was writen to OceanDNA-b17183/target_genomes.txt
[2023-03-16 05:27:37,652] [INFO] Task started: fastANI
[2023-03-16 05:27:37,652] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ddbd28-17e1-4a77-9e65-f681f5fd8c38/OceanDNA-b17183.fa --refList OceanDNA-b17183/target_genomes.txt --output OceanDNA-b17183/fastani_result.tsv --threads 1
[2023-03-16 05:27:45,702] [INFO] Task succeeded: fastANI
[2023-03-16 05:27:45,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:27:45,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:27:45,707] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:27:45,707] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:27:45,707] [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
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	78.9381	215	672	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	78.8607	219	672	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	78.8243	232	672	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	78.8128	216	672	95	below_threshold
Lacrimispora algidixylanolytica	strain=SPL73	GCA_003609635.1	94868	94868	type	True	78.6209	223	672	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:27:45,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17183/tc_result.tsv
[2023-03-16 05:27:45,713] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:27:45,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:27:45,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference/checkm_data
[2023-03-16 05:27:45,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:27:45,721] [INFO] Task started: CheckM
[2023-03-16 05:27:45,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17183/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17183/checkm_input OceanDNA-b17183/checkm_result
[2023-03-16 05:28:20,022] [INFO] Task succeeded: CheckM
[2023-03-16 05:28:20,023] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 13.89%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-16 05:28:20,301] [INFO] ===== Completeness check finished =====
[2023-03-16 05:28:20,302] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:28:20,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17183/markers.fasta)
[2023-03-16 05:28:20,303] [INFO] Task started: Blastn
[2023-03-16 05:28:20,303] [INFO] Running command: blastn -query OceanDNA-b17183/markers.fasta -db /var/lib/cwl/stga7314590-0205-444a-bde2-0233f70278d5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17183/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:28:20,923] [INFO] Task succeeded: Blastn
[2023-03-16 05:28:20,924] [INFO] Selected 18 target genomes.
[2023-03-16 05:28:20,924] [INFO] Target genome list was writen to OceanDNA-b17183/target_genomes_gtdb.txt
[2023-03-16 05:28:20,982] [INFO] Task started: fastANI
[2023-03-16 05:28:20,982] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ddbd28-17e1-4a77-9e65-f681f5fd8c38/OceanDNA-b17183.fa --refList OceanDNA-b17183/target_genomes_gtdb.txt --output OceanDNA-b17183/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:28:34,239] [INFO] Task succeeded: fastANI
[2023-03-16 05:28:34,247] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:28:34,247] [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
GCF_003833015.1	s__Lacrimispora sp003833015	91.5097	622	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013036995.1	s__Lacrimispora xylanolytica_A	79.649	280	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934545.1	s__Lacrimispora xylanolytica	79.54	307	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	98.92	98.92	0.97	0.97	2	-
GCA_015057775.1	s__Lacrimispora sp015057775	79.5335	246	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057715.1	s__Lacrimispora sp015057715	79.5081	289	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009712635.1	s__Lacrimispora sp009712635	79.4493	290	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057705.1	s__Lacrimispora sp015057705	79.1758	269	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732605.1	s__Lacrimispora celerecrescens_B	79.063	216	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	96.56	95.54	0.85	0.79	5	-
GCF_000526995.1	s__Lacrimispora indolis	78.9905	228	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.32	99.25	0.95	0.92	3	-
GCA_002367105.1	s__Lacrimispora sp002367105	78.9732	206	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363835.1	s__Lacrimispora sp902363835	78.9498	223	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797975.1	s__Lacrimispora celerecrescens	78.9381	215	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.58	99.58	0.96	0.96	2	-
GCA_002429965.1	s__Lacrimispora sp002429965	78.7144	207	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	99.06	99.06	0.84	0.84	2	-
GCA_900105215.1	s__Lacrimispora sphenoides_A	78.65	233	672	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	97.72	97.62	0.92	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-16 05:28:34,247] [INFO] GTDB search result was written to OceanDNA-b17183/result_gtdb.tsv
[2023-03-16 05:28:34,248] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:28:34,249] [INFO] DFAST_QC result json was written to OceanDNA-b17183/dqc_result.json
[2023-03-16 05:28:34,249] [INFO] DFAST_QC completed!
[2023-03-16 05:28:34,249] [INFO] Total running time: 0h1m10s