[2023-06-05 18:51:52,639] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:51:52,642] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:51:52,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference
[2023-06-05 18:51:54,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:51:54,156] [INFO] Task started: Prodigal
[2023-06-05 18:51:54,156] [INFO] Running command: gunzip -c /var/lib/cwl/stg31de022b-aa6a-4459-b210-cbf3947f4112/GCA_934293475.1_ERR7745425_bin.26_genomic.fna.gz | prodigal -d GCA_934293475.1_ERR7745425_bin.26_genomic.fna/cds.fna -a GCA_934293475.1_ERR7745425_bin.26_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:51:58,111] [INFO] Task succeeded: Prodigal
[2023-06-05 18:51:58,112] [INFO] Task started: HMMsearch
[2023-06-05 18:51:58,112] [INFO] Running command: hmmsearch --tblout GCA_934293475.1_ERR7745425_bin.26_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference/reference_markers.hmm GCA_934293475.1_ERR7745425_bin.26_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:51:58,375] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:51:58,377] [INFO] Found 6/6 markers.
[2023-06-05 18:51:58,411] [INFO] Query marker FASTA was written to GCA_934293475.1_ERR7745425_bin.26_genomic.fna/markers.fasta
[2023-06-05 18:51:58,412] [INFO] Task started: Blastn
[2023-06-05 18:51:58,412] [INFO] Running command: blastn -query GCA_934293475.1_ERR7745425_bin.26_genomic.fna/markers.fasta -db /var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference/reference_markers.fasta -out GCA_934293475.1_ERR7745425_bin.26_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:51:59,086] [INFO] Task succeeded: Blastn
[2023-06-05 18:51:59,093] [INFO] Selected 17 target genomes.
[2023-06-05 18:51:59,094] [INFO] Target genome list was writen to GCA_934293475.1_ERR7745425_bin.26_genomic.fna/target_genomes.txt
[2023-06-05 18:51:59,095] [INFO] Task started: fastANI
[2023-06-05 18:51:59,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg31de022b-aa6a-4459-b210-cbf3947f4112/GCA_934293475.1_ERR7745425_bin.26_genomic.fna.gz --refList GCA_934293475.1_ERR7745425_bin.26_genomic.fna/target_genomes.txt --output GCA_934293475.1_ERR7745425_bin.26_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:52:05,960] [INFO] Task succeeded: fastANI
[2023-06-05 18:52:05,961] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:52:05,961] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:52:05,966] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:52:05,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:52:05,967] [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
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	78.4248	105	544	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	77.4453	67	544	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	77.4389	65	544	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:52:05,969] [INFO] DFAST Taxonomy check result was written to GCA_934293475.1_ERR7745425_bin.26_genomic.fna/tc_result.tsv
[2023-06-05 18:52:05,969] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:52:05,969] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:52:05,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference/checkm_data
[2023-06-05 18:52:05,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:52:05,996] [INFO] Task started: CheckM
[2023-06-05 18:52:05,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934293475.1_ERR7745425_bin.26_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934293475.1_ERR7745425_bin.26_genomic.fna/checkm_input GCA_934293475.1_ERR7745425_bin.26_genomic.fna/checkm_result
[2023-06-05 18:52:26,525] [INFO] Task succeeded: CheckM
[2023-06-05 18:52:26,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.89%
Contamintation: 1.85%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:52:26,551] [INFO] ===== Completeness check finished =====
[2023-06-05 18:52:26,552] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:52:26,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934293475.1_ERR7745425_bin.26_genomic.fna/markers.fasta)
[2023-06-05 18:52:26,553] [INFO] Task started: Blastn
[2023-06-05 18:52:26,553] [INFO] Running command: blastn -query GCA_934293475.1_ERR7745425_bin.26_genomic.fna/markers.fasta -db /var/lib/cwl/stgba0f7454-9e98-4d8c-b60a-60954d7702dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934293475.1_ERR7745425_bin.26_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:52:27,354] [INFO] Task succeeded: Blastn
[2023-06-05 18:52:27,360] [INFO] Selected 17 target genomes.
[2023-06-05 18:52:27,361] [INFO] Target genome list was writen to GCA_934293475.1_ERR7745425_bin.26_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:52:27,471] [INFO] Task started: fastANI
[2023-06-05 18:52:27,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg31de022b-aa6a-4459-b210-cbf3947f4112/GCA_934293475.1_ERR7745425_bin.26_genomic.fna.gz --refList GCA_934293475.1_ERR7745425_bin.26_genomic.fna/target_genomes_gtdb.txt --output GCA_934293475.1_ERR7745425_bin.26_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:52:34,888] [INFO] Task succeeded: fastANI
[2023-06-05 18:52:34,900] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:52:34,900] [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_900766925.1	s__CAG-127 sp900766925	78.1836	135	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938485.1	s__CAG-127 sp017938485	78.0748	115	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017517305.1	s__CAG-127 sp017517305	77.8688	123	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057525.1	s__CAG-127 sp015057525	77.8493	126	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057515.1	s__CAG-127 sp015057515	77.8464	85	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463225.1	s__CAG-127 sp017463225	77.8057	107	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625335.1	s__CAG-127 sp017625335	77.6675	105	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017625815.1	s__CAG-127 sp017625815	77.6437	94	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553925.1	s__CAG-127 sp900553925	77.4106	69	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.14	96.66	0.89	0.85	4	-
GCA_017480195.1	s__CAG-127 sp017480195	77.3559	99	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014799405.1	s__CAG-127 sp014799405	77.1711	96	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057445.1	s__CAG-127 sp015057445	77.0548	100	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464045.1	s__CAG-127 sp017464045	76.9047	59	544	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:52:34,903] [INFO] GTDB search result was written to GCA_934293475.1_ERR7745425_bin.26_genomic.fna/result_gtdb.tsv
[2023-06-05 18:52:34,903] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:52:34,908] [INFO] DFAST_QC result json was written to GCA_934293475.1_ERR7745425_bin.26_genomic.fna/dqc_result.json
[2023-06-05 18:52:34,908] [INFO] DFAST_QC completed!
[2023-06-05 18:52:34,909] [INFO] Total running time: 0h0m42s