[2024-01-24 10:49:34,260] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,262] [INFO] DQC Reference Directory: /var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference
[2024-01-24 10:49:35,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:35,504] [INFO] Task started: Prodigal
[2024-01-24 10:49:35,504] [INFO] Running command: gunzip -c /var/lib/cwl/stg93206186-c0ad-4b0a-8f1b-2a32eea3966b/GCF_900258535.1_PRJEB24722_genomic.fna.gz | prodigal -d GCF_900258535.1_PRJEB24722_genomic.fna/cds.fna -a GCF_900258535.1_PRJEB24722_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:51,843] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:51,843] [INFO] Task started: HMMsearch
[2024-01-24 10:49:51,844] [INFO] Running command: hmmsearch --tblout GCF_900258535.1_PRJEB24722_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference/reference_markers.hmm GCF_900258535.1_PRJEB24722_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:52,257] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:52,258] [INFO] Found 6/6 markers.
[2024-01-24 10:49:52,314] [INFO] Query marker FASTA was written to GCF_900258535.1_PRJEB24722_genomic.fna/markers.fasta
[2024-01-24 10:49:52,314] [INFO] Task started: Blastn
[2024-01-24 10:49:52,314] [INFO] Running command: blastn -query GCF_900258535.1_PRJEB24722_genomic.fna/markers.fasta -db /var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference/reference_markers.fasta -out GCF_900258535.1_PRJEB24722_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:52,962] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:52,966] [INFO] Selected 11 target genomes.
[2024-01-24 10:49:52,967] [INFO] Target genome list was writen to GCF_900258535.1_PRJEB24722_genomic.fna/target_genomes.txt
[2024-01-24 10:49:52,973] [INFO] Task started: fastANI
[2024-01-24 10:49:52,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg93206186-c0ad-4b0a-8f1b-2a32eea3966b/GCF_900258535.1_PRJEB24722_genomic.fna.gz --refList GCF_900258535.1_PRJEB24722_genomic.fna/target_genomes.txt --output GCF_900258535.1_PRJEB24722_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:05,177] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:05,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:05,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:05,198] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:50:05,199] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:05,199] [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
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	100.0	2054	2054	95	conclusive
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	94.1084	1306	2054	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	94.1078	1316	2054	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	94.102	1317	2054	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	85.1627	1322	2054	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	85.058	1332	2054	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.9671	91	2054	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.6293	93	2054	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.5481	134	2054	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	76.4538	66	2054	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	75.9927	69	2054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:05,204] [INFO] DFAST Taxonomy check result was written to GCF_900258535.1_PRJEB24722_genomic.fna/tc_result.tsv
[2024-01-24 10:50:05,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:05,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:05,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference/checkm_data
[2024-01-24 10:50:05,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:05,265] [INFO] Task started: CheckM
[2024-01-24 10:50:05,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900258535.1_PRJEB24722_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900258535.1_PRJEB24722_genomic.fna/checkm_input GCF_900258535.1_PRJEB24722_genomic.fna/checkm_result
[2024-01-24 10:50:56,339] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:56,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:56,372] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:56,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:56,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900258535.1_PRJEB24722_genomic.fna/markers.fasta)
[2024-01-24 10:50:56,376] [INFO] Task started: Blastn
[2024-01-24 10:50:56,376] [INFO] Running command: blastn -query GCF_900258535.1_PRJEB24722_genomic.fna/markers.fasta -db /var/lib/cwl/stg443e8d43-92d2-4aec-be3d-e19ce92c7d6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900258535.1_PRJEB24722_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:57,470] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:57,475] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:57,476] [INFO] Target genome list was writen to GCF_900258535.1_PRJEB24722_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:57,497] [INFO] Task started: fastANI
[2024-01-24 10:50:57,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg93206186-c0ad-4b0a-8f1b-2a32eea3966b/GCF_900258535.1_PRJEB24722_genomic.fna.gz --refList GCF_900258535.1_PRJEB24722_genomic.fna/target_genomes_gtdb.txt --output GCF_900258535.1_PRJEB24722_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:08,088] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:08,104] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:08,104] [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_002270465.1	s__Blautia hominis	98.397	1675	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.84	98.04	0.89	0.81	4	conclusive
GCF_001689125.2	s__Blautia pseudococcoides	94.102	1317	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.82	99.56	0.97	0.91	7	-
GCF_900461125.1	s__Blautia coccoides	85.2278	1356	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.33	97.47	0.84	0.79	11	-
GCF_014287615.1	s__Blautia sp001304935	84.9691	1347	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCA_003481745.1	s__Blautia stercoris	78.3787	209	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCA_900765525.1	s__Blautia pullicola	77.4323	199	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.10	98.67	0.84	0.76	4	-
GCA_900556555.1	s__Blautia sp900556555	77.4301	127	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112785.1	s__Blautia stercorigallinarum	77.3334	206	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.88	99.88	0.94	0.94	2	-
GCA_019114545.1	s__Blautia pullistercoris	77.2672	186	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.87	98.79	0.80	0.76	4	-
GCA_019116105.1	s__Eubacterium_I avistercoris	75.7367	52	2054	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.96	99.96	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:08,105] [INFO] GTDB search result was written to GCF_900258535.1_PRJEB24722_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:08,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:08,109] [INFO] DFAST_QC result json was written to GCF_900258535.1_PRJEB24722_genomic.fna/dqc_result.json
[2024-01-24 10:51:08,109] [INFO] DFAST_QC completed!
[2024-01-24 10:51:08,109] [INFO] Total running time: 0h1m34s