[2023-06-08 20:36:34,089] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:34,092] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:34,092] [INFO] DQC Reference Directory: /var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference
[2023-06-08 20:36:35,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:35,502] [INFO] Task started: Prodigal
[2023-06-08 20:36:35,502] [INFO] Running command: gunzip -c /var/lib/cwl/stgbacbee0b-8d3b-45bb-a875-1fd22a0320fc/GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:41,614] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:41,614] [INFO] Task started: HMMsearch
[2023-06-08 20:36:41,614] [INFO] Running command: hmmsearch --tblout GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference/reference_markers.hmm GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:41,876] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:41,877] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbacbee0b-8d3b-45bb-a875-1fd22a0320fc/GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-08 20:36:41,902] [INFO] Query marker FASTA was written to GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:36:41,902] [INFO] Task started: Blastn
[2023-06-08 20:36:41,902] [INFO] Running command: blastn -query GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference/reference_markers.fasta -out GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:42,494] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:42,499] [INFO] Selected 27 target genomes.
[2023-06-08 20:36:42,499] [INFO] Target genome list was writen to GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:36:42,501] [INFO] Task started: fastANI
[2023-06-08 20:36:42,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacbee0b-8d3b-45bb-a875-1fd22a0320fc/GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:59,412] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:59,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:59,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:59,419] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:59,419] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:59,420] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.7128	99	650	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.1955	51	650	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	75.8648	50	650	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:59,422] [INFO] DFAST Taxonomy check result was written to GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:36:59,423] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:59,423] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:59,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference/checkm_data
[2023-06-08 20:36:59,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:59,458] [INFO] Task started: CheckM
[2023-06-08 20:36:59,458] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:37:23,678] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:23,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:23,702] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:23,703] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:23,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:37:23,704] [INFO] Task started: Blastn
[2023-06-08 20:37:23,704] [INFO] Running command: blastn -query GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc24f14a1-5a0d-455f-ad93-6cd2bf8b5b46/dqc_reference/reference_markers_gtdb.fasta -out GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:24,535] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:24,541] [INFO] Selected 14 target genomes.
[2023-06-08 20:37:24,541] [INFO] Target genome list was writen to GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:24,542] [INFO] Task started: fastANI
[2023-06-08 20:37:24,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgbacbee0b-8d3b-45bb-a875-1fd22a0320fc/GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:33,286] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:33,304] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:33,304] [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_011959105.1	s__Acetatifactor sp011959105	98.5895	610	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.00	99.00	0.85	0.85	2	conclusive
GCA_910585015.1	s__Acetatifactor sp910585015	81.2551	421	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910583845.1	s__Acetatifactor sp910583845	80.7795	421	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577235.1	s__Acetatifactor sp910577235	80.2739	379	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584375.1	s__Acetatifactor sp910584375	80.2629	380	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014804645.1	s__Acetatifactor sp014804645	80.1383	387	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624175.1	s__Acetatifactor sp017624175	79.1316	242	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586215.1	s__Acetatifactor sp910586215	77.1637	117	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584865.1	s__Acetatifactor sp910584865	76.9116	96	650	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:33,306] [INFO] GTDB search result was written to GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:33,307] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:33,310] [INFO] DFAST_QC result json was written to GCA_949121985.1_ERR4467335_bin.6_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:37:33,310] [INFO] DFAST_QC completed!
[2023-06-08 20:37:33,310] [INFO] Total running time: 0h0m59s